Back again with a few more:

On a Seraphis: Based on fly: as annoying as a fly, as easy to kill as a fly.
On a Mara: Based on a squashed cockroach, with guns, yuck!
On a Boanerges: Based on: ok, I have no idea what we were drinking that day.
On a Pegasus: How's my stealthing? 1-800-GTVA, hey, wait!
On a Pegasus: I respect your privacy...
On Alpha 1 ship: God made Earth in 7 days, I killed everything in 6 shots.
On Alpha 1 ship: It's not what guns you have, it's just how you shoot.
On Alpha 1 ship in the last mission: So many targets, so little time!
On Alpha 1 ship again on the last mission: This would be really funny if my subspace drive was working.
On any wingman: I'm not as think as you drunk I am.
On any ship in a nebula: Don't follow me. I'm lost too.
On a shivan ship: Learn from your past mistakes, dont f*** with shivans!
On a GTVA ship: If this ship is flying right it's been stolen. Help!
On a shivan capital ship: If we're coming your way, dive! Dive! Dive! Hit your burners, pilot!
On a Zeus: Heavily under-armored for your safety.
On a GTVA capital ship: If at first you dont succeed, shoot again.
On a Hatsheptsut: We have no hats, sheeps nor suits.