If I really had to choose one, it would have to be Majora's Mask. Absolubtly loved that game, every single minute of it. I'm not even goig to start giving examples, because I'd be here All Night (Mask - hee hee).
In no particular order for runners up though: Ocarina of Time, Rouge Squadron and Battle for Naboo (I liked it!), Goldeneye, Star Fox: Lylat Wars (I think that's the right one? It's been a very long time...) and Star Wars: Podracer.
(I was going to be all funny unbearable and say Superman 64, but some jokes simply shouldn't be made. I'm pretty sure I could be banned from this site and legally executed in seven countries even for saying this much...)