In no particular order:

a) TF2. It's kind of funny - TF2 is basically a combination of all kinds of things I normally feel either pretty neutral about or hate (it's the only online 'shooter' I play). And yet, it's been one of my go to time killers/stress relievers since beta.

b) Giants: Citizen Kabuto. There was room for improvement with this game, by a lot, actually. But the overall gameplay and design will have me forever mourning that we'll never see a sequel/remake.

c) Baldur's Gate II - Hands down the best hack and slash RPG ever brought to a game.

d) System Shock 2 - Cliche maybe. But damn, few games have been so good when they were released.

e) Diablo 2 - getting dated fast in my opinion (in fact, I stopped being able to enjoy it a fair bit ago), but absolutely brilliant.

honorable mentions:

Beyond Good and Evil - excluded solely because it was primarily marketed to consoles. One of the best examples of game design ever made.

Total Annihilation - Dune 2 gets a lot of (rightful) credit on the RTS front, and even C&C gets some. But TA showed what forethought and polish could do to the design of RTS, and it's also one of the few games that is an RTS as much as it's an RTT.

Half Life - amazingly new immersive story telling. nuff said.

Planescape: Torment - This game reminds me some of Fallout, in the way that they threw out a lot of conventions and said "No. It's going to be great our way." and it was.

Privateer - As much as I played Tie Fighter, this was the better game at the end of the day (if not the better space combat sim).

Bard's Tale - Sup graph paper.