Weapons - when destroyed, capship turrets fire less frequently and less accurately, and fighter weapons cannot fire
Communications - when destroyed, fighter cannot send nor receive messages
Sensors - when destroyed, fighter cannot target ships
Navigation - when destroyed, ship cannot jump out (only if AI Profiles entry is active)
Engine - when destroyed, ship cannot move nor turn
Hangar - when destroyed, capship cannot launch fighters
All other subsystems (ie. Reactor, Bridge, etc) have no effect unless something is triggered upon their destruction in FRED, such as the 'Crystal' subsystem on the Shivan Comm Nodes in "Into the Lion's Den" (triggers self-destruct)