Seriously, these games actually felt like episodes of the series - they were compelling as hell, with real storytelling, application of logic and problem-solving.
'A Final Unity', was also very similar, but TNG-era.
Later games, like Elite Force, Armada, and stuff, while good from a gameplay perspective, didn't really feel like Star Trek, at all, or if they did, they just felt like later seasons of Voyager, i.e. pretty far from the exploration and awe that Trek is about. If anyone is into retro games, I urge you to play them.
If I were to rank Trek games, best to worst...
1). Judgement Rites
2). 25th Anniversary
3). A Final Unity
4). Klingon Academy
5). Birth of the Federation
6). Klingon Honor Guard
7). Generations (rare game now)
Hopefully the new 'Gears of Star Trek' third person shooter will be good - they seem to be putting some thought into it, and it could flesh out the movies and the new Enterprise quite well.