Important VSU technologies and corresponding visual aesthetics
Armor
Impact, ablative, reflective - laminated alternating layers or just one or more of the above. Shield-induced deformations of incoming ordinance may make traditional shaped-charge approaches obsolete. Needs to still withstand shrapnel/debris. Needs to provide protection from EM and neutron radiation. Significant materials questions abound. Presume that significant advances in materials science have been made over the next 1200 years, but no scrith, no neutronium armor, and no "living armor", although some groups (Rlaan, client species) may use substances produced by living organisms in the construction of their vessels.
Crewed Compartments
Military Cockpit:Quite possibly filled to the brim with an oxygen carrying liquid (for oxygen breathers) that circulates through the suit (except in event of damage where suit will start using internal reserves). This will allow the pilot to withstand higher accelerations, but precludes standard stick-jockey seating - the pilot should be lightly and flexibly tethered. Also functions as the escape pod. Getting into and out of the cockpit quickly not the top priority. Probably only habitable portion of vessel.
Visually, this means that, somewhere as far from the engines/reactors as possible in a cramped design, is a more-than-person-diameter spheroid with a life support system, a whole network of sensor connections, and enough explosive bolts to shove it away from a dying ship. For many groups, probably covered in indirect optical lenses, but never "windows" (see: sensors). The particular appearance of the hull around this cockpit/eject pod would vary by the aesthetics of the group manufacturing it. <Aside: Mechanists will be outliers here (pilot can already fulfill many functions of a self-contained eject pod - just needs additional supplies).>
Civilian Cockpit:Possibly same as military cockpit, but also likely to be a more low-key strap-and-cushion affair with simple atmosphere. May connect to other crewed portions of ship, if such exist. May also contain fuzzy dice and hirsute co-pilots.
Passenger areas: Strictly low-acceleration. Except on luxury craft or observation lounges, probably somewhat sheltered from the most external portions of the ship, when possible - think airplane seating. Common areas/lounges more likely to have significant window-age. Located as far away from reactors, engines, and other dangerous bits of the ship as possible.
Command and Control (Military Bridge): On larger, low-acceleration craft, think Battlestar Galactica C&C - armored bunker in middle of ship. As accelerations go up, still an armored bunker, but with progressively less flexibility in crew movement during maneuvers. NOT A CONNING TOWER, NOT AN ISD BRIDGE. Capital vessels not piloted fighter style or via window (use sensor plots, see: sensors section below), no need for big, vulnerable target for beheading. Still, even armored bunkers have beheading problems - several potential damage vectors may leave a small diameter cylinder of damage with long penetrating length. Thus, such structures are likely to be redundantly constructed in larger vessels, and be designed for crewing in suits during combat.
FTL Drives
I'll start simply: nobody knows what these should really look like, because they are figments of our imagination. Moreover, as they won't correspond to anything real, the visuals need only not contradict the described functionality, without much worry about how things actually work (because they don't actually work). In particular, what the externally visible parts should be is quite open for imagining.
Here are some rough guidelines - but in the end, be creative and I think whatever falls out will probably be workable.
In-system: We're still in the process of probably ret-conning how this works a bit, but with respect to size, whatever the in-system FTL drive ends up being, it'll be small enough to mount on a 30-meter craft. We're currently considering something that will allow the player to travel through some sort of altered representation of space, perhaps with regions of different resistances to travel (analogs to currents or underlying topologies ?) and possibly to transition between different particular strata within this altered representation, so no portal devices as such, but more likely some sort of tearing/bubble/something drive. May want some sort of widgets on outside to represent whatever is manipulating space around the ship. Tech is intended to be related to shield-generation principles and gravitic weaponry. Perhaps just uses shield emitters in different mode? In either case, should have similar aesthetic, once one is chosen for either. Scaling with respect to ship size should be considered - denser arrangements on small craft than on larger, distributed over much of hull?
Jump (outsystem): This device, like the in-system drive needs to be able to fit on a 30-meter craft (in it's most miniaturized form). I envision it as being more of a cost and complication issue than pure bulk and size - possibly much easier to build the same system in a larger format for a larger ship. Not as common a device (too expensive, too power hungry). This is probably the most complicated piece of tech on the entire ship - but it's probably also mostly internal. If you can see too much of the jump drive from outside, something has probably gone badly for you. Mostly, you can think of it as a door-knocking device - the jump system itself (not built by extant species) takes care of the heavy lifting (via principles somewhat understood at this time in the VSU timeline, but by particular means not as yet discovered (happens later), i.e. there's no discernible physical gate structure, just a point in space with odd properties)., flinging you from one end to the other.
Reaction Drives
With the exception of the Rlaan, everyone else uses fairly intuitive, and visible drive systems to go traverse normal space. Small quantities of matter exit in directed fashion at extremely high velocity, providing thrust. Reaction drives are not particularly friendly things - if we ignore for the moment made-up techs, such as FTL and shields, it is clear that the highest-energy consuming part of any normal vessel will be it's engines, and consequently, it's not a good idea to be near them when they're on. Thus, there should be a clear path from any primary thruster away from a vessel - it shouldn't cook itself when the pilot floors it. For finer-grained work, such as docking, it should be presumed that a secondary set of very small, weak, thrusters are present at various points around the ship ( see, for example, the small thrusters in the FRONT END of the space-shuttle).
Being able to stop and being able to turn are very important. This means that there need to be thrusters of similar aggregate strength (and therefore similar visual importance) on both ends of each axis of thrust. Different axes may have very different strengths, but both ends of a single axis should be balanced in most designs. Center of mass is also something to consider for engine placement. If all of the engines are on one side, the ship will spin, thus, asymmetry in the ship will likely translate to asymmetry in the thruster arrangement.
Visually speaking, a single thruster is probably going to look something like a cross between a rocket nozzle and the business end of a linear particle accelerator. As long as it's clear that there's a hole and some coolant circulation and some sort of support widgets that look like they could be responsible for keeping the exhaust stream from actually touching anything on the way out, it's probably on the right track. Different groups will probably have slightly different aesthetics - more or less beveled nozzles, embedded exit points flush with the ships skin, or clearly external arrangements, etc. Likewise, some groups will use more, smaller exit points, and others fewer and larger. Civilian approaches could (perhaps) be modeled as having larger engines for the same thrust generation (greater safety margins, lower wear) ?
The size of the exit hole should be actually fairly small compared to the whole exit assembly.
Engines will generally be closely coupled to one or more reactors - often both as the source of energy and the source of propellant.
Rlaan drive should still be thought of as technically a reaction drive, but extremely distributed in the presentation of where the reaction is being effected. Still not particularly friendly to be around. Assume thrust on a Rlaan ship can be applied at the same level in any direction at any particular time - this will influence Rlaan ship design, even if the thrusters as such aren't actually as visible. Also assume Rlaan drive tech to be shield-tech related. Rlaan "thrusters" should look like modified Rlaan shield emitters.
Reactors
The number one visual property of reactors is that they are large, and every ship has at least one. Larger ships will almost certainly have more than one. Even smaller ships may have a small, backup reactor, but it will bear little resemblance to the actual heart of a ships power - think of any backup reactor of this sort as more like your car battery: it can keep the lights on and the radio going (and in this case, the oxygen going), but you're not driving anywhere on it. Even the cleanest fusion reaction throws off a bit of neutron radiation. Thus, distance and physical shielding should separate the reactor and the crewed area to the degree possible (in a 30 meter craft... not so much :) ). At least one reactor will be directly slaved to the thrusters, and the smaller the ship, the more integrated the arrangement. They are the pumping heart of a ship, and protected accordingly. If you shoot one enough, it won't go Chernobyl, but it will leak plasma all over the place and stop working. Reasonable reactor shapes include spheres and toroids, or collections thereof - but most of the space devoted to the reactor is probably going to be empty spaces inside the reactor, massive cooling and plasma channeling equipment on the outside of the reactor, shielding between the reactor and other vital bits, and means of shunting fusion exhaust out to an engine to be expelled. One possible setup would simply have one reactor per primary thruster, or grouped set of primary thrusters (completely slaved). In this configuration, it may be best to think of such reactors as part of the engine they are attached to, and then the "reactor" as just the reactor being used to provide power to all of the ships weapons and shields and other systems.
Visually, given the protection generally afforded such an important component, the distinguishing external features would probably be the size, shape, and locations of the bulges (perhaps a telltale set of corrugated torroids one abutting the next jutting out of the rear of one group's ships, or spherical bulges in the midsection for the vessels of another group). The reactors would be at their most naked in strike craft, especially in-system and cheaper builds. A sense of danger in piloting the craft can be implied by the degree that the reactor is depicted in an exposed state. Still, even given the need for protection, it'll be a high-maintenance item, so even the best protected reactor has to have some accessibility. Perhaps there will be easily identifiable massive armored hatches on the distinctive bulges that help reinforce the "reactor behind here!" visual message.
Civilian vs. military can also be exemplified by how separated the crew/passenger/cargo bits of a ship are relative to the engines/reactors.
Sensors
All sorts of sensors required, from visual (cameras and optical fibers) to radio to "gravitic" *cough* and lidar and so on. 1200 years hence, we're not going to fly a spaceship by staring out a small glass window and aiming for the north star. That said, it's not clear what all of these sensors will look like, so it's probably best, even if a bit anachronistic, to deploy enough whisker antennae, parabolic direction transceivers, radar geodesics and dark lenses to give the impression to a modern viewer that the ship has sensors of one form or another that probably cover something close to a 360 degree sweep.
For luxury vessels, or observation decks, the window + eye is still a sensor option, but not the preferred military choice. Indirect optical, say, through optical fibers rather than opto-electrical connections (such as cameras) may be deployed to give some sort of filtered illusion of looking out through a particular portion of a vessel (perhaps especially true in small craft) without relying on an entirely computer-generated display or cutting big holes in your armor that are transparent to lasers (if you can see them through the window, they can lase you through the window :-P). Some habits will die hard, and some groups, though still augmenting their display with data from all the other sensors, will still want to be able to rely on as direct an optical feed as is possible.
Shields
VS shields in this time period are imperfect in their ability to block damage, and how they affect incoming attacks depends greatly on the type of attack (thus, armor is still important). They are presumed to function, in part, on similar principles to the FTL drives and "gravitic" weapons. There is also presumed to be an integrated EM component to shielding (hence GEM for Gravitic-ElectroMagnetic shields). Visibly, they're clearly something that will be seen on the outside of the ship, and may have a hierarchical distribution on larger ships. What exactly they look like is going to be an area of significant creative license, but should be consistent within a single manufacturing group, and similar in some ways to the FTL and gravitic weapons aesthetic. There should probably be complete, if not uniform, sense of coverage by the emitters over all portions of a ship's exterior.
Shield <-> matter reactions are presumed violent. Shield <-> shield reactions are presumed to mitigate this. If you want to dock with another vessel, some negotiation of lowering all or portions of the shields will have to occur.
System Preferences (briefly)
The Rlaan are odd, they don't use missiles, they do use lots of single-use drones. Rlaan love "exotic" weaponry (see: Weapon techs) and point-blank engagement ranges.
The Aera like to make hits count. This biases weapon selection toward shield-penetrating options such as lasers and complex penetration-oriented warheads despite drawbacks in efficiency and cost - but not to completely irrational levels.
Not everything should be a carrier. Having docking facilities for a shuttle/pinnace does not make a ship a carrier. Every sufficiently large ship should have some associated shuttle/pinnace. Not every ship, even larger ones, needs to be able to internally dock arbitrary small craft (external docking likely on those without internal docks).
Not every ship has super-awesome special weapons. Many just have different numbers or logical scaling extensions of the same weapons used on other ships.
Related: Not every ship will be equally kickass against a given threat profile.
Related: Not every ship will be kickass
Related: For every class of kickass combat ship, there will be multiple classes of logistical support vessels
Related: The total number of active classes of vessels is limited
Weapon Placement (briefly)
Briefly - turrets, turrets, turrets. With the exception of small craft (craft turns to turn weapons) and role-specific weaponry (weapon size proportional to vessel size, by construction), it's going to be a lot easier to move the gun than turn the ship. Missile launchers get this mostly for free.
Point defense - because that incoming missile won't shoot itself down. Completely blind spots not desirable, but coverage not necessarily uniform.
Weapon Techs
The one thing that is true across all weapon systems, excepting those, that like missiles, are detachable or expendable, is that there must be some mechanism to deal with the inefficiencies of the system, manifested as heat. At least some part of most weaponry will probably be swaddled in cooling mechanisms - if your widget is only 50% efficient in delivering energy to the enemy, hope that either your time component or area component is vastly different, or you'll be hurting yourself as much as the target. Alternatives to heavy cooling machinery (probably just coolant piping, the actual radiators could be elsewhere) include self-contained, expendable heat-dump coolant as part of the ammunition package, or systems, such as missiles, that deal with cooling independently.
Disabling
Most weapons designed to cripple, rather than destroy, will actually be small, precise versions of one of the other damage types, but a few particular instances come to mind.
Blinding
Broad spectrum EM - a combination of noise emitters from the radio through the UV - would look like a bunch of antennae and some bright lights.
EMP
Outside of an atmosphere, making an EMP device is a bit more complicated, but probably involves explosives and coils.
Very High Voltage Arcing (Think "space-taser")
At the range that this would work, either some of their sensors or deeper electronics will fry, or you'll spot weld your weapon-system to their hull. Either way, something is going to happen, but you'll need to be in knife-fighting range to use it. May make more sense for civilian security drones or certain pirate vessels than anything else.
"Exotic" (Gravitics, shield-tech and other made up things)
Looks like.... whatever we decide it looks like. There's probably a business end of the weapon, but likely not a hole. Should probably look similar, if scaled, across weapons from the same major group, and different across weapons from different major groups, (say, Aera vs. Rlaan, but less so for Andolian vs. Unadorned). Should bear some resemblance to other technology making use of the same (imaginary) "principles", such as the FTL drive or shield emmitters. This should be the most esoteric, high-tech looking piece of Rube-Goldberg-ism that we see among the different armaments.
Explosive
Assume, for smaller warheads, that they are minature fusion devices. Normal explosives wouldn't be much use (better to just use kinetic impact). Normal explosives might be used to set up a dispersal pattern (for shrapnel/bomblets). Otherwise, assume various sizes of (laser-induced) fusion devices (they're relatively clean) and the occasional high-end device featuring anti-matter. Bomb-pumped lasers will feature a fusion-warhead, but will focus the destructive output into a small number of coherent beams rather than an expanding shell of x-rays. (FWIW, in vacuum, it's the x-rays that will likely do most of the nuke damage, with damage going as 1/r^2). Visually, not that profound looking - a roughly spherical, opaque warhead surrounded by whatever auxiliary equipment is used in the delivery device, sensors, or armoring.
Kinetic
Space fights can still have big long gun barrels. Mass drivers(aka coil guns) and rail guns are the likliest suspects. The longer the gun, the more oomph these can probably pack. On a smaller craft, the ship might end up being built around a single one of these weapons. Shorter barreled versions will still be functional, but less effective. Diameters will likely be fairly small - the mass of the projectile is less important than the exit velocity. Note that the equal and opposite reaction issue applies here - if the mass driver is too far off center, or not balanced with another similar weapon, the recoil will spin the ship about its axis, as well as push it in the opposite direction of the projectile. While not guaranteed to hit anything at range, the nice thing about kinetic weaponry is that they're just as effective at 50000 kilometers as at 5 kilometers.
Lasers (and other coherent radiation weapons)
Lasers are the likeliest candidate for turrets rather than spinal mounts on a small craft. See: current ABL project. The laser device itself could be developed in the bowels of the vessel, and then routed to the appropriate exit point. Laser range is determined by wavelength and diffraction. The size of the emitter influences diffraction and is itself heavily influenced by the wavelength of the laser. Rough rule of thumb - for a given wavelength, bigger emmiter, longer effective range. Even if there is a single, well-defined exit point and general direction (which, for efficiency, there may well be for offensive lasers) there still will be no barrel or other immediately "gun-like" protrubance. More recognizeable features would tend closer to parabolic dishes, concentrators, antennae, and such than gun barrels. Laser rifle, for instance, is an oxymoron (rifling a laser guide makes no sense). Lasers are notoriously ineffecient, and thus will have some of the largest cooling systems.
Missile
Missiles come in one of a few sub-forms:
Bomb
An immobile or mostly immobile warhead, lobbed at the enemy. If deployed definsively, may also be same as mines. Damage mechanism can be kinetic, (if released from a fast moving delivery platform) or one of the other types. Visually, will look like warhead sans delivery system, probably with sensor package, unless kinetic warhead.
Dumb (rocket)
A small, single short-burn drive unit coupled to a warhead. The missile will rapidly accelerate toward the target in one short continuous thrusting phase, after which, it behaves similarly to a bomb. Often deployed from tightly packed modular rocket pods (visual cue: attack helicopter rocket pods) for short range saturation fire (i.e. can't miss scenarios or to disperse tight formations/ deny particular avenues).
Long-range Kinetic
A long-range weapon for deployment against immobile targets. It goes into a a long, slow, acceleration phase, until it either reaches a point where it can no longer significantly change its vector, or runs out of fuel or coolant. Such missiles are dense, heavily armored, and don't have any means of stopping (all tail-thrust, modulo initial maneuvering).
Short-burn (missile)
Even more stripped down than a long-range kinetic missile, these do, fundamentally, resemble miniature ships, but with all of the cooling aparatus minimized or absent, and any fancy in form replaced by the need to be tightly packed. They are tail-heavy in thrust, but highly maneuverable, thus requiring thrusters on axes. They are skeletal in construction. They must withstand high accelerations at arbitrary angles in order to effectively intercept targets, but must reduce mass at all costs to achieve those accelerations. Thus, they are internally stable, but very fragile with respect to outside forces. They will doggedly pursue a target until detonation, destruction, or drive failure. Lacking meaningful cooling mechanisms and with minimal fuel supplies, these missiles have relative short active runs, although some can have much longer ranges through coasting phases.
Long-burn (torpedo)
Only a few steps shy of a ship in miniature, it is not particularly more manueverable than a small craft (and is, like most missiles, tail-heavy in thruster arrangement), and, especially given the expense of one, not designed to target them. Torpedoes are designed only to target larger vessels, and need only out-accelerate them. To that end, they are equipped with real drive and cooling units, capable of propelling massive warheads within range of their targets, along with sophisticated sensors, countermeasures, and penetration aids. These will almost always have fusion warheads or greater, and will often be designed to detonate as soon as they are within nominal damage range, rather than wait for true optimal, as their targets will be both wily in their ECM and deadly in their point-defense.
Capital Missile
In all respects but crew, reuse, jump drive, and thrust equality (they are tail-heavy) a capital missile a strike craft in miniature. Often rivaling an in-system strike-craft in size, these behemoths are carried in quantity only by capital vessels or fixed installations, and only deployed against capital vessels, sometimes from distances so great that they will need to make use of in-system FTL drives for full effect. Many variants of these delivery platforms exist, some even mounting their own missile deployment systems. Visually, these are the most complicated incarnations of missiles, and, along with (to a lesser degree) the torpedoes, the only missiles large enough to warrant attention to hierarchical details.
Particle
More efficient than a laser, but subject to both thermal and electrostatic bloom, limiting range as a function of exit velocity. If going fast enough, doesn't matter too much what the particles were. Longer runs can give better acceleration. Can come in linear accelerator or synchrotron format. Forms of the latter can be quite large (think Large Hadron Collider) and smaller craft would not be able to mount beams of both heavy particles and high exit velocities. Particle beams (of opposite charge) may be paired and merged before exit to avoid charge-buildup issues, at the expense of efficiency (i.e. two of everything except the business end of the gun). For linear accelerators, longer is probably a good indicator of beefiness. For circular, diameter is the key indicator - the center can also be hollow - only the ring matters.
Projectile Warhead
Delivery system as per smaller version of kinetic (doesn't need to achieve same high velocities) or even more conventional gunnery, with payload as per bomb. Think: Artillery shell and associated launching hardware.
Plasma
It's not a gun. It's a flamethrower. Your engines may also be considered as being in this category. Possibly good for when you don't want to harm the interior of the vessel too much (at knife-fighting range) but of limited military value due to bad 1/r^2 properties. Anything moving fast enough to avoid dispersion effects looks more like a pulsed version of a particle weapon, and would be better considered as such.