I kind of like this idea I'll see if I can come up with a few others:
When you make a hit and run action you may forgoe your command check instead to attempt and hack the target ships vox channels. Once aboard make a +0 Tech Use check in place of the command check to hack the enemies Vox's aboard the ship making communication impossible until repaired. While under the effects of malfuctioning voxes the targets crew rating drops by 2 + 1 per degree of success on the tech use check.
You make your way to the shells of one of your macro batteries and make a +0 demolitions test. Success means you rig extra explosives to key shells causing them to do +1 damage +1 more per 2 degree's of success when next fired. Failure causes something to go wrong and makes the macrobateries rigged unable to fire for one round. Failure by 5 or more degree's means something terrible happens and the rigged shells go off in the ship, the ship immediately suffers 1 hit from the macrobaterries through armor and void shields and the component becomes damaged (similarly a GM may rule a player doing this action must burn a fate point).
When you make a hit and run action you may forgoe your command check instead to "capture" enemy soildiers and offer them to join your crew in exchange for their lives. To do so make a +0 intimidate check in place of your command check, success takes 1 crew rating from your opponent +1 per 2 degree's of success and transfers those points to your own ship but drops your own ships morale by half the crew pop gained.
Hope this spurs some idea's, I'll post again if I think up any more.