Half Life 2. This game is flawless, the overall experience is just completely fluid, and Valve did an excellent job of blending the gameplay with story development. The game never had a moment in it that felt terribly forced or awkward for me, not even the physics puzzles. After I got done with this game I felt completely satisfied. Not too short, not so long that it's boring. And the game had variety thrown in there too, with shooting, puzzles, driving, and even that level where you control the antlions (which is a blast by the way. I just love this game.
Fallout 1. Unlike Fallout 2, the entirety of this game was perfect, and the pacing was excellent (though I didn't think it was as good towards the very end). I wish that the gameplay was more varied than shoot the enemy in the eyes all the time, which is probably the only thing holding this back from being the most perfect game of all time. Fantastic game overall.
Starcraft. I'll be honest, I'm horrible at RTS games. I don't play them much, I'm bad at them, and I don't enjoy them that much. But as far as RTS games go, this one is the best. As a game for casuals it's varied, fun, and easy to pick, but it also has a lot of depth for competitive play. Fantastic RTS.
But honestly I don't think there's a perfect game. There's games that I think are shining examples of their genre (Starcraft, Guilty Gear, Fallout) but none of them are perfect.