I couldn't decide on just 5, so here's my top 10:

01. The Legend of Zelda: Ocarina of Time
02. Star Fox 64
03. Goldeneye 007
04. Super Mario 64
05. Mario Kart 64
06. The Legend of Zelda: Majora's Mask
07. Super Smash Bros.
08. Mischief Makers
09. Turok: Dinosaur Hunter
10. Star Wars: Rogue Squadron

Ironic that my two top favorite N64 games just happen to be the two N64 games they remade on the 3DS.