1. Quake. Not for the single player mind you, or even the multiplayer, but rather the multiplayer mods the game spawned. Notably, Team Fortress. To this day my favorite interpretation of Team Fortress was Quake's Team Fortress Mega (a mod of team fortress).
2. Deus Ex. It is my favorite game of all time so it would be a shame not to put it on the list.
3. Mechwarrior 4. Yes, Mechwarrior 2: Mercs was probably the best game in terms of the campaign. Yes, Mechwarrior 3 was probably the best computer game interpretation of the Battletech rules. But the changes in MW4 (that I originally hated) resulted in a game that actually worked online. Unfortunately, the FASA rules sort of rely on the notion of a significant chance of missing the target and the inability to deliver all the rounds in a volley to a particular spot. This basically resulted in one shot kills in MW3 and was not a lot of fun as a result.
Notable others:
Icewind Dale
Fallout Tactics
Baldur's Gate Saga
Neverwinter Nights 2
Dawn of War 2
Ground Control
Total War series
Freelancer
Descent
Doom
Duke Nukem 3D
Quake 3
Unreal Tournament (series)
Tribes
Vampire the Masquerade: Bloodlines
