are you talking on a fighter or cap ship?
on a fighter, i think the sensors disables your targeting, not certain though, never happened to me
and i think nav disables the radar, again, guessing, engines are obvious, and i'm not certain about the rest, if there is any, this is purly guess work
Sensors disable radar and targeting, nav prevents you from jumping out but nothing else, comms damage garbles radio transmissions (it adds random gaps in the text and random static in the voice) or will totally stop radio messages if destroyed. On a capship, destroying engines doesn't decrease speed
proportionately; it reduces the ship's max speed slightly until all engines are destroyed, but even with 1 engine ships go almost at their normal full speed. Killing Weapons on a capship has no effect other than the blob turret example already mentioned, but weapon subsys are normally fairly weak so I take them down just for the hell of it.
Some other ships have unique subsystems. Usually they have no effect on gameplay, but you can FRED in different effects. Some ships have radar dishes. The Faustus has a solar panel subsystem: kill this and the panels stop spinning and look damaged. The infamous ShivanCommNode has a blade subsys and a crystal subsys. Killing the blades stops them from spinning, obviously, and killing the crystal makes the thing loose hull integrity rapidly (giving you time to escape the shockwave). Finally, the NTF Boadicea (the NTF asteroid) is cool because it has a whole bunch of different subsystems, such as Barracks, Command Tower, life support, and so on. People say that the model looks like crap, but there are still cool subsystems to kill.
In the model-making utilities you can put any kind of subsystem- bridge, fighter bay, cocktail bar- but only weapons, nav, and engines will have an ingame effect, unless the mission designer made it so, say, enemy reinforcements would stop coming if the comm subsystem is destroyed.
That was
way too long. Well, question answered?