Well, I can only comment on the one's I have actually played, so...
Star Fleet Academy:Strategic Command from Interplay was a so-so game that came out quite some time ago. A little flashy, but you got to drive a star ship! I only got the first 8 levels in this box edition though.
Birth of the Federation by Microprose. A good turn-based strategy game, and one that lets you run an empire. If your into that it is a fairly nice game.
Star Trek: Away Team from ActiVision, Squad based strategy with ship board and planetary missions. I liked this one fairly well, as your team member choices effected the out come of your missions. I would recommend it.
Dominion Wars by Simon & Schuster Interactive. A real-time tactical strategy game. I really got into this one, and I consider it the best of these four. So it recieves my vote!