Paper Mario. I loved that game so much. I think it might have been the very first video game I've ever beaten. The two N64 Zeldas are tied for second place, though.
I had many great hours with Star Fox 64. Majora's Mask and Kirby 64 were great as well. And I don't care what anyone says,
F-Zero X > Star Wars Pod Racing > Diddy Kong Racing > Mario Kart 64
Hey You Pikachu! or Pokemon Snap. I don't think I played anything else as much as I did those two besides Bomberman Hero and Star Wars Rogue Squadron (?).
It's hard to say, growing up, I really enjoyed a lot of games on the N64. But I have to say my all time favourite, and it was the first one I ever completed by myself as well, was Banjo-Kazooie.
It was funny, it was beautiful graphics-wise (I mean, it probably can't be considered so much now, but considering the time it was made, it's lovely), it was easy to play and remember the controls. The music was great, and beating Gruntilda was just an epic feeling for me.
Both Zelda games. I didn't even exist when Ocarina of Time was released, and I couldn't even speak when Majora's Mask was, but I played them both and loved them anyway.