Judgement Rites and 25th Anniversary were great, to my shame I have to admit that I have never played A Final Unity even though I own it. For some reason I never got it to work on my PC when I bought it in the 90s. I really should put some effort to getting it to work some day and play it.
I remember spending a lot of time with Starship Creator when I was a kid. I remember having fun with it even though it would crash constantly on my PC. Star Trek Generations was not too much to my liking back then, but i did play quite much when considering that I was not too fond of it.
The games that I absolutely loved were Star Trek Starfleet Academy (PC) as well as the FMV-games Star Trek Klingon and Star Trek Borg. Because of Klingon and Borg I still have a soft spot for all FMV games, my guilty pleasure.