This thread would be challenging if we were not allowed to mention Rare. That company was almost the reason to own an N64; Goldeneye, Perfect Dark (fuck the haters this game was better), Conkers, and to lesser extent the Banjo games (they were collect-a-thons...not totally my thing).
Not counting those two companies I'd say the AKI wrestling games were amazing for their time (leagues ahead of the shitty acclaim/iguana titles). Shadows of the Empire was a blast when it came out, haven't played it in nearly a decade though so not sure if it has held up. Mischief Makers has aged pretty well too, it is a game that is pretty easy to beat, but to get really high ranks is another story. I only beat it just two years ago and was blown away by how fun it was. That game makes me realize that the N64 really should have been a console for quality 2d titles. Perfect for the cart format.
Can't recall if Wayne Gretzky's 3d hockey is good anymore. Has been nearly 15 years since I played that title.
Almost everything else is forgetable