Honestly, I tired every Star Trek Game that came out.
But the three that I keep going back to are:
Star Trek: The Rebel Universe (On a related note, anyone know a good program to slow my computer down so this game doesn't end five minutes after I start it?)
Star Trek: The 25th Anniversary
Starfleet Command: Orion Pirates
The rest of the games are too poorly done to play for any length of time. (and god how I wish that Birth of the Federation was STABLE! Brilliant game, good concept, sloppy coding.) I honestly don't expect this game to be any different, add the Play to Pay factor and this may be the first ST game in a long time that I just avoid altogether.
For The Rebel Universe, have you tried Dosbox (
http://www.dosbox.com/)? I've had luck with it running games from the late 80s/early 90s. It is made to emulate the best Dos conditions, including sound.