For me I would say the main one is the ocean in WW - it was a fresh and brilliant adventure!
But here's a more recent one: New Super Mario Bros. U.
In NSMBU, there's a sense of wonder again, of exploration and discovery. New Super Mario Bros. U fully recaptures the spark of Mario's 2D heyday, something the wii and 3ds titles fell short on. But people point it out as a game that is just more of the same old 2d mario and 'Ain't nobody got time for that!'. I think that the mere existence of NSMBW and NSMB2 (both rather mediocre titles) are what is holding people back from seeing the true masterpiece that is NSMBU (I absolutely love that game for what it is).
Change the art style, music, and name and this game would be hailed as a classic masterpiece.
Games can and should tell stories and share ideas through their mechanics. This is the intrinsic element of the medium and this is how experiences should be crafted in video games. No company does this as well as Nintendo and their echoes from the past.
Aurum Ring 
Delano7 
Ocarinahero032
