Might as well choose a few off the top of my head
Mischief Makers - A strange game, it's either love or hate. I loved it.
Bomberman 64 - Crazy hard puzzle/action game. I call it a part puzzle because later levels require a LOT of thinking/bomb jumping, expecially if going for 100%.
Bomberman 64: The Second Attack - More action than 64, but less puzzling.
Goemon's Great Adventure - One of my favorite 2D platformer's on the N64. Amazing music, visuals, and gameplay.
Mystical Ninja Starring Goemon - Very different from above, as it's a 3D adventure game, but still amazing for all the same reasons.
Legend of Legaia - Brutal RPG that has an interesting battle system and doesn't focus on grinding as much as other RPG's. It obviously helps, but is completely possible to beat without if played smart.
Harvest Moon: A Wonderful Life - On of my two favorite Harvest Moons. Farmin', minin', marryin' and all the rest.
Digimon World - Got good reviews, but nobody has ever heard of it. Raise Digimon, explore the island, battle others for them to join and help the town, Digimon dies, rinse and repeat. Extremely addicting. Needs to be remade.
Pokemon Card Battle - The only Pokemon card game on the market. We need more Pokemon Cards!
Harvest Moon: Friends of Mineral Town - Basically a clone of PS harvest moon, but portable!
Dragon Warrior Monster 2 - A Pokemon like raising system mixed with Dragon warrior battle system. I poured hours into this game when I was younger.
Muramasa: The Demon Blade - A 2D sidescroller with Okami-like graphics, special moves, and easy to learn, hard to master gameplay.
F-Zero GX - Come on, even though this site loves this game, nobody outside Gamecube enthusiasts have even played this game. My favorite racing game of all time.
May post some later if I think of them.