In my opinion Star Trek and Star Wars had both good and bad games pretty equal amount. There have been some awful Star Trek games (like Hidden Evil) but most of the games have been playable if not exactly good. I have enjoyed most of the star trek games that I have played. 25th Anniversary and Judgement Rites are probably the best ones, A Final Unity I have not played as i have never been able to get it working. I too wish that those three games would be playble with ScummVM.
As far as other games that I have enjoyed, I really liked the FMV games Star Trek Borg and Star Trek Klingon. Yeah they were a bit clunky, but I enjoyed them nonetheless. Starfleet Academy was really good as well. Birth of the Federation I played a lot, and that is on my top list as well.