LEt's see...
There is the stability systems,the anti-gravity generator,the thrusters,airbrakes,weapon bays,artificial intelligience,and maybe even the ship-pilot integration interface.
For the stability systems,maybe an off-centre mass due to a projectile hit would make things slightly difficult.
For the anti-gravity generator,rubbing against the floor because of a generator shutdown is very annoying,yet interesting.
Anyone see the intro for WipEout where a ship blows the exhaust? Maybe a weapon could cause a clog up,which would require the accel to be held down for it to be blown off(potential shrapnel effect?)
Having airbrakes jammed(unusable or always on) would be VERY annoying...
A ship with a disabled weapon bay in a weapons on race=sitting duck
Artificial intelligience could be made stupid like the Pilot Assist in HD because of a scramble in programming.
A totally black screen(ie pilot knockout) may cause rage quits...