I can definately re-reccomend system shock 2. One of my Favourite games of all time. Cyborg Mid-wives.... sweet jebus, wear brown pants.
Deus Ex 1. My actual favourite game of all time. Just superb in every way, a must play. Don't play the sequel though, it was developed in parrallel for the x-box + PC and got shafted for it. (Hope that doesn't foreshadow the Development of F3 for the 360 and PC)
Interested in RTS's? Total Annihilation still holds up today. Great fun, still got active community on the go.
The X-Com series, again. X-Com apocalypse will run on modern PC's more easily than the first two. I rather liked UFO Aftermath and Aftershock. The Real Time combat took some getting used to but once you did it was serviceable.
A few people have mentioned Galactic Civillisations. Very good game, but if you like that and want to go real "hard core" (i hate myself sometimes) then try Space Empires IV, available over Steam. Epic galactic conquest game with almost endless possibilites, very complex at times, and micromanaging hell gets in the way in mid-late game.
Master of Orion 2, is the most enjoyable Civ type game i have ever played, a bit dated now (Ok very dated) but still amazingly playable, will suck your life away. (Don't play MOO 3 though, utter tripe)
Thats all i can think at the moment, it's early and i need coffee.
Cheers
Sven