I've got Armada 2, Bridge Commander, Voyager: Elite Force, and Conquest on the PS2. Love 'em all. USS Defiant mod for BC is so wonderful.
Best Star Trek games I played were:
Star Trek Judgement Rites
Star Trek 25th Anniversary
Star Trek: A Final Unity
Oldschool eh:)
EDIT: Also liked the Elite Force 2 where I had the chance to wander around in Enterprise and interract (on a MINIIIIIIMAL level) with Picard and his crew.
Never played a star trek game. But im deffinatly playing cryptics Star Trek Online when it comes out next year.