Off the top of my head...
Ocarina of Time
Majora's Mask
Super Mario 64
Mario Tennis 64
Ogre Battle 64
Rayman 2: The Great Escape
Banjo-Kazooie
Banjo-Tooie
Donkey Kong 64
Super Smash Brothers
Space Station Silicon Valley
Excitebike 64
Starfox 64
Beetle Adventure Racing
Pilotwings 64
Star Wars: Shadows of the Empire
Star Wars: Pod Racer
Rogue Squadron
Turok Dinosaur Hunter
Turok 2
Goldeneye 007
Perfect Dark
Conker's Bad Fur Day
Paper Mario
Castlevania 64
Mario Kart 64
F-Zero X
Resident Evil 2
Sin and Punishment
borderline cases...
Hybrid Heaven
1080 Snowboarding
Jet Force Gemini
Blast Corps
Bomberman 64
Castlevania: Legacy of Darkness
Doom 64
Glover
Goemon's Great Adventure
Harvest Moon 64
Vigilante 8
I thought Megaman 64 was fun too, but many others said it was crap

Really, the N64 had plenty of good games if you knew where to look. Its one flaw was the complete lack of RPGs. There was Quest 64 (a steaming pile), Aydin Chronicles (ditto), and Ogre Battle 64 (a great game that was more strategy than rpg).