I don’t know if this counts, but the Star Trek: The Next Generation pinball machine was pretty damn good.
loved 25ah anniversary. However, I'm going to go very old school and say one of my favorites growing up was a game called Begin. It was set in the star trek universe and was a starship combat simulation. It was all text based but really fun. They had a pretty fleshed out system of weapons, shields, power and so forth.
Starfleet Command is my definitive gold standard for ship simulator combat games. SFC:OP was the definitive version. They mucked it up with the sequels. Most of my Trek gaming is on the tabletop. Star Trek the deck builder from Bandai is memorable for me because I love narrating my turns as I play them out. Star Trek Ascendancy was on my hotness until a little bit ago (theme too much of a pasted-on thing). Star Trek Fleet Captains was also good until the cross-era unfocused nature of the game annoyed me so I made my own alternative. I also did a smidge of Attack Wing, before the card shenanegans and the Borg got too much for me.
Probably Star Fleet Academy, followed by Starfleet Command and Klingon Academy as while I like Feds more, it had some improved gameplay mechanics over SFA.
Mine would have to be the one that was never finished: Star Trek: Secret of Vulcan Fury because it showed what could have been. As Spock himself said, "there are always possibilities."
25th Anniversary and Judgment Rites were my favorites until Klingon Academy came along. Played a lot of EGA Trek back in the day, if that counts. Really enjoyed the writing in the Promethean Prophecy game, felt like I was in one of those Star Trek novels. Can't play any text game now without falling asleep. Played a few Star Trek games in the 80s, not because they were necessarily good, but because it's all we had.
I only got to play them a few years after they came out - only really becoming a Trekkie as a teenager in about 2002 - but I loved to death Starship Creator and Starfleet Command, although I've never been much good at tactics. I liked Starship Creator a bit more as I loved coming up with ideas for crew combinations and ship designs. I was a big fan of Tom Paris, so always made him captain of any ship I made.