Off the top of my head some of my favorites are:
Duke Nukem 64
God I played this game to death. I remember spending countless hours with my friends just playing in the death match. Had some awesome cheat codes aswell to keep things entertaining. Was close between this and Goldeneye 007 for N64.
Legend of Zelda : OOT
What can I say about this game that hasn't already been said. Started when I was just a little kid watching my mom and dad play zelda on nes. Didn't really get into it until OOT was released on N64.
Day of the Tentacle
Awesome game with a great story and cast of characters that really got me hooked on point and click games. (Could be said about any of the Lucas Arts point and click games really)
Super Mario 64
Just another amazing Mario game.
Im leaving out tons but you get the idea.