I feel Donkey Kong 64 doesn't get much attention or praise. It deserves more. I find it criminally underrated among fans. It got good scores and such, but many gamers didn't like it. It's no DKC, and it has some annoying flaws, but it's a damn fun game with great graphics. The bosses are especially awesome and epic.
I also like Rayman 2. Seems to be you've either heard of it or you haven't. I think many people forget about it. The N64 i believe was the base system they developed it for. It was multiplatform, but in a way, the N64 version might be the most impressive version when you consider the system capabilities. It's amazing looking for one, with an incredibly smooth framerate that NEVER drops below 60fps. It controls really well too. And it's just fun to play. Yeah, back when Ubisoft didn't suck and we didn't have the rabbids raping the franchise, those were the days...
I've not played much of it yet, but i'd like to play more of Jet Force Gemini. It seems to be very fun and is a fine third person shooter/adventure/action game. Only weird thing is that for a Rareware game, the graphics aren't as good as their other N64 games. But it seems to have a lot of heart. I've played very little of the game so far, but it is fun so far. Probably pretty rare too, i never originally heard about it until i got into N64 emulation.
Resident Evil 2 is pretty much a perfect port of the PS1 game, voice acting, video, and all that stuff. Amazing what they crammed on a 64MB cartridge considering the game originally took up 2 CD's. It has high resolution support with the expansion pack too, so it looks a fair bit better than the PS1 version too. Shocking indeed. I'd actually take this version over the PS1 game.
Diddy Kong Racing is a fun alternative to Mario Kart. It had a DS port which was hit or miss. The N64 game has a slightly less smooth framerate, but it controls better and has all the features intact. Too much was cut or butchered in the DS port if you have access to and N64.
Kirby 64 i find to be a fine sidescroller. It had a hit or miss reception as well, but it's certainly a nice game. The powerup combinations are awesome. In most Kirby games, you can eat enemies and steal their powers. Here though, you can combine TWO powers together to make a totally new power. For example, eat a spike enemy, then toss the power at a fire enemy. You then get a flame sword. There are TONS of combinations you can try, and that alone makes the replay and gameplay worth it. It's up there as one of the better Kirby games. Maybe not enough to beat Super Star or the Dreamland games, but well up there in rank. Fine game on its own merits.
I've barely tried these other games, but they've been recommended highly and are apparently great games- Space Station Silicon Valley, Mickey's Speedway USA, Mischief Makers (Treasure-developed platformer apparently), Glover, Chameleon Twist 1 and 2, Duck Dodgers Daffy Duck, Rocket- Robot on Wheels, and Shadow Man. I've played a few of those in limited form. They seems to be fun games, most of them, but i can't speak much for them yet. There was also a PS1 game called 40 Winks (3D platformer) that was going to be released for the N64 as well. Someone found an unreleased completed cart of it and dumped it online not too long ago. It's virtually identical to the PS1 version, but you might like it. I've tried it, it's not bad. Not great, but a decent enough game. Only available online though...
Long post i know, but there are a lot of unknown N64 gems out there.
BTW, this topic would probably be more fitting here-
http://gbatemp.net/index.php?showforum=165