Ah, a compelling thread! Let me see... well, yeah, it's fairly difficult for me to consider any game--or any thing--"perfect", but I'll give you some top contenders:
"Perfect"
Shadow of the Colossus: Great aesthetic, combined with an arguably unparalleled synthesis of gameplay and symbolism-laden storytelling. I mean, if you've played this, there's not much else I've got to say.
The Legend of Zelda: Majora's Mask: Proof that you can make an awesome (Zelda) game in about a year. Has all the elements of a great modern adventure game, with an emphasis on people like I've never seen.
The Legend of Zelda: Twilight Princess: Haters gonna hate--this is still the most bang for my buck I think I've ever gotten in years of gaming. Did it do anything groundbreaking? No, but it didn't need to.
God of War III: Well, it's epic, the graphics are great, there's plenty of variety, it ties the trilogy together pretty well... nothing to complain about here!
Near-"Perfect"
Metroid Prime: Everything, from the atmosphere to the interface, to the very fact that this game managed to be as great as it was in the first place, is top-notch. It's just... well, that Omega Pirate really had me snarled for a while. But I was young... dunno, maybe I should bump this up to "Perfect".
Uncharted 2: As far as "cinematic" games go, I've never seen its equal. Would I want all the games I play to be like this? Of course not, because it's also derivative as sin and mildly repetitive... but what a show!
Ico: I'd put it right up there with SotC, but Yorda is not always the easiest to deal with. I suppose that's partly intentional, though--and everything else about the game is so stunning.
Braid: The art, music, and gameplay are wonderful... now, if it wasn't deliberately confusing, it could be slightly better.
I'm sure there are entries for both of these lists that I'm forgetting at the moment, and so I apologize. Part of it is because I'm realizing that there is a difference between "favorite" and "perfect" games--for example, Chibi-Robo and Mario & Luigi are two of my favorite games, but describing them as "perfect" seems... off.