Here are some of my picks. Some are more under the radar than others:
Bomberman Hero: One of the best OSTs from that generation secretly exists within this random 3D action/puzzle platformer.
Bomberman 64 (J): Not to be confused with the Bomberman 64 that came out here, the Japanese Bomberman 64 is a traditional 2D Bomberman game. It’s a fitting game for the system which is synonymous with 4-player games.
Mystical Ninja Starring Goemon & Goemon’s Great Adventure: Two solid Goemon games on the platform. The first is a more open 3D platformer while the latter is a 2D platformer.
Doom 64: This has gained some notoriety over the past couple years but it’s a pretty damn good original Doom game and runs surprisingly well. Be sure to max out the brightness settings in-game because it’s dark as hell in places.
Super Smash Bros. (J): Not under the radar by any means, but if you haven’t played the Japanese version, it has different fighting sound effects (more hard-hitting and less bowling alleyish, beam sword sounds like an actual lightsaber, etc) and some other differences here and there. Pretty neat to play if you’re a fan of the Western release.
Castlevania 64/Legacy of Darkness: These kind of have a meh reputation, but I don’t think they’re that bad. They pale in comparison to the Zelda games on the system camera/controls-wise, but they’re neat, atmospheric action/adventure games with quite a bit of ambition.
Harvest Moon 64: Many consider this to be one of the best Harvest Moon games. As someone who hasn’t played too many of the other games, I couldn’t tell you what makes this better than the others, but I think it’s a fun game on its own either way.
I’ve got more but I’ll just go with these for now
PS: Put me in the camp that thinks N64 on consumer CRTs via composite doesn’t look bad.