Underrated, as in didn't do as well as they deserved games:
System Shock 2 (If it had done better, LGS would still be here!)
Project Eden (One of the last decent 4-player co-op FPs-style games. Actually its more like a 3D version of Lost Vikings set in the future...)
Armed and Dangerous (It's basically Giants: Citizen Kabuto, only sicker, funnier and harder! )
BattleZone (It's an RTS crossed with an FPS with vehicles!! So ahead of its time... Driving a hover-tank has never been so fun, and someone needs to port the RAVE GUN!! to FS2... Only thing that comes close is BZ2, but that's nowhere near as good, although the community fixes make the game a LOT better)
Tribes: Vengence (Actually, this sucked compared to Tribes 1 and 2, but the storyline was pretty epic)
Anachronox (Plays like Squaresoft RPG; Damned funny. IMHO the best game that Ion Storm made)
Planescape:Torment (Buggiest piece of crap I've ever played, but the game is just so damned epic... and deep...)