Starfleet Command 2 is my personal preference for that series, and it's probably the best 'ship centered' Trek game. That said, it's based on Star Fleet Battles more than Star Trek, and some Trek fans seem to have a certain intolerance for that.
Oldies but goodies to dig up are Star Trek: 25th Anniversary or Star Trek: Judgment Rites. That's only if you like adventure games, though.
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"Stop sounding battlestations just to hear the alarm."
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