Klingon Academy was a lot of fun, really enjoyed 25th Anniversary and Judgement Rites as well. Elite Forces was another great one, I enjoyed SFC I, II, and III, but those games weren't everyones cup of tea. Bridge Commander was fun too. The mods for Klingon Academy and Bridge Commander really pro-longed those games for me.
Really enjoyed Strategic Operations Simulator, and Rebel Universe...but that's probably more a nostalgia thing than anything else. Promethean Prophecy was really good, but not many people can tolerate text based games, but it genuinely felt like I was apart of TOS in a way no other game has.