I had a friend who had 25th Anniversary and I never got a chance to play A Final Unity but the one I got the most enjoyment out of was that old mainframe one. I had a version on my Commodore 64 and loved hunting down Klingons with those state-of-the-art ASCII graphics.
Yeah, Dosbox works wonders. Final Unity is the best, followed by 25th Anniversary and Judgement Rites. I fantasize at least once a week of a Mass Effectish Star Trek game. I even had a dream about it once, it was amazing.