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.)
My vote goes to Shadow of the Colossus. The story, the mood, those damn creatures. Just enough frustration to keep you going and enough variation to not make it boring.