I believe The Beatles: Rock Band came the closest to being perfect. Eveything about that game was just beautifully done and the only things missing was Pro Drums, an option for Keys, and a few more Beatle songs (Hey Jude, Strawberry Fields Forever, Yesterday etc. etc.)
Gotta be Portal 2. The puzzles are fun, the difficultly curve is reasonable, and the writing is fantastic. Truly the only complaint I have is that I wish there was more of it.
What I really like is that it is never unfair. Once you understand what has to be done, it is easy to accomplish. So it is a great kind of difficulty. And there is more: The free mod “Portal reloaded” is really great.
It’s not Portal 1 or 2. I’m sure of this because I and others think Portal is possibly the best example of a perfect game and lots of other people say it was good but Portal 2 was a perfected version (and the opposite is also true, I think Portal 2 is good but lost a lot of what was wonderful about Portal.)
My point being, it’s so commonly contentious about which of the two was perfect and which one was merely good but not quite to the standards of the other that it must be that either is only subjectively a perfect game. Though, in fairness, possibly there are no objectively perfect games, but in that case the question really just comes down to “what games do you think are good?”
When I think of perfect games I think of Portal 2