Depends what we go by...
Single player games I like to beat every few years: Zelda games, DKC games and most 2D Mario plataformers... my favourites in these categories would probably be OoT (LttP is a close second though), DKC2 and SMW. If we count the NES/SNES FFs as Nintendo games then those too.
Single player games I grinded and spent endless hours on due to their high replay value and time-killing entertainment: Starfox 64. And if you count GB's Tetris, then that too.
Multiplayer games I loved playing with my friends: every MK and SSB (out of these two I'm more of a MK guy). Also the fighting games in SNES (Clay Fighter, Killer Instinct, DBZ games, and especially SF2), and I absolutely loved N64's Goldeneye multiplayer mode.
Oh, and as a bonus: Mystical Ninja: Starring Goemon for the N64. It's a game that just makes me happy... I love the ambience, soundtrack, originality and the cheesy humour. While you can't say it's one of the N64's best games due to the amazing catalog the system has, it's still highly underrated and it's a game I very much enjoy and replay once every few years.