Damn, that's a hard question. There are several that come to mind for me.
Tom Clancy's Splinter Cell: Chaos Theory is one of my favorites. The game is just so well designed, and still holds up today in spite of it's age. In particular, the AI is actually really good (Which is key for a good Stealth Game.) and the controls are actually really good on the PC. I was expecting to have to rebind them, but they're really comfortable. In all honesty I enjoyed this game way more then Metal Gear Solid, though some people would kill me for saying that, haha.
Another Game that I loved is Half-Life. This game is so well designed that it's beautiful. The Level design in particular is amazing. At no point in the game did I get stuck for very long because of the balance in difficulty. It's easy enough for you to figure out, but challenging enough to really make you think. And the storytelling is actually really good, in spite of the rather straightforward plot. And gives some moments in the story much more impact then they would otherwise have. And the enemies are really well designed too.
Final Fantasy 7 is easily my favorite Final Fantasy game. I really loved the game's story, and there were some unexpected plot twists in there. It's a really good JRPG, and I think it's one that's definitive of the Genre. Some may disagree with me on that, but that's my honest opinion. The game hasn't aged all that well though, which does really suck. But it's still a great game.
Megaman X, is also up there. It's an extremely well designed game that teaches you how to play without actually having a tutorial. It teaches you through the game itself. But you could watch Egoraptor's sequelitis on the game. He explains it better then I can.
And lastly, Castlevania: Symphony of the Night. I, love, this, game. But I don't want to write another paragraph explaining why. X(