Zelda: Ocarina Of Time really is magnificent. I'd heartily recommend Majora's Mask too, but it's a bit of a marmite game.
OoT is one of the few games that really thought about what you could do with 3D, rather than just adding an extra dimension for marketing purposes. The Forest Temple, with its rotating corridors, is one of my top gaming things ever.
Worth noting that you'll need a rumble pack to enjoy both of those to the full, and an expansion pak for Majora's Mask.
I've not played them personally, but Blast Corps, Jet Force Gemini and Paper Mario get a lot of lip service.