I just now replaying System Shock 2 on my recently aquired Windows 98 PC, and it is such a fantastic game.
I enjoyed it a lot when I first played it many years ago, but I was pretty new to the whole FPS thing (and definitley to FPS/RPG hybrids) so I didn't get as much out of it as I could have. The two or three times I played deep into it back then was as a marine.
Now I'm playing as a Navy guy, and it's a completely different game. I realize I didn't even scratch the surface of the depth that's in SS2.
I even think the graphics are pretty good, although whoever did the character models should be tarred and feathered. They're WAY inferior to rest of the visuals.
Other candidates:
Baldur's gate (the first one)
Fallout
Thief
NFS:high stakes
Alpha Centauri