@JGZInv: WiH and WoD r2's are already using these, so I assume there's an elegant, non-interface-screw way of doing this even without a proper implementation.
Sabotage subsystem, Shield anihillator pulse, Shield restore, Telepathic attack (temporary lowers target AI to lowest class), Telepathic conversion (changes target IFF), Repair bots (as healing, but can be used on other friendly targets), Subspace inhibitor field projector (temporary makes target unable to jump), Tactical microjump (changes player position coordinates in the viewing direction + 5000 m, and adds jump effect).
Customizing turret weapons before mission would be also very cool 
Sabotage subsystem and Shield annihilator pulse sound too much like weapons- if those are available, why would I have weapons that do the same thing? But they could be useful.
Shield restore is a good one.
Telepathic attack and telepathic conversion seem sort of like something the electronic warfare suite could do to drones or turrets, but some ability to affect normal ships would be interesting as well.
Repair bots sounds nice. Deploy them, maybe they heal any fighter within 200m at a steady rate.
Subspace inhibitors seem like they'd break missions unless they could only affect ships below cruiser or freighter size. Could be doable with a well-designed mission that considers it though.
Tactical microjump.. hmm. I actually have an idea for an FTL system, not related to FSish in-system jumps. that allows travel at long distances but with not much precision. Once you entered it, most of the screen would look like a HUD showing icons for ship locations and planet orbits, and you'd move around sort of like in that ME2 thingy, then exit at roughly your new position. I dunno how either it or tactical microjumps would work as a module though since it seems like a mission based on it would require it.
A couple more ideas I had:
Control assault drones: If a friendly capship releases a wing of assault drones to assist, you could take control of the wing leader and give orders to the rest of the drones. The drones would be faster and more powerful than your fighter but much weaker, so you can use them temporarily to great effect but they go down quick. This would leave your own fighter a sitting duck, though; maybe the effect would have to be canceled automatically as soon as you take damage.
Proximity mines: Yes, a blatantly offensive one, I know, but not necessarily one that can be easily replicated using primaries or secondaries. Would drop mines (kamikaze ships with a mine model, maybe the countermeasure model if one is not available) that would home in on any enemy ships within 300 meters or so. (I've been wanting this in FS since I last played Descent)
Stealth: Hides your ship from enemy sensors until you get within 500m of an enemy ship. Works the first time, can be activated again once you evade with limited probability of success.
EMP reduction: Reduces the effect of EMP from weapons and/or nebulae storms.
