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.)
I think it gets harder for a game to be perfect as it increases in complexity and scope. I think games like Tetris and Guitar Hero are good examples of games that are basically perfect, but that’s partially because they’re so simple.
In terms of more complex games, I think some Mario games could be described as perfect. I remember Super Mario Galaxy 2 being basically flawless. (Although it’s been so long since I played it so maybe it had some flaws that I don’t remember).
Also personally I might argue that Rollercoaster Tycoon 2 is flawless.