Banjo Kazooie and Tooie.

Great 3D platformers - I actually prefer them over Super Mario 64.

Paper Mario. I loved it more as a kid, but I still love it now. The atmosphere is amazing, and the gameplay mostly holds up.

Great picks! The 64 may have had a small library overall, but damn if it didn't pack a ton of greatness into that small library.

Banjo Kazooie gets my personal pick; I actually rank it above Mario 64 as I feel it perfected the formula that Mario pioneered. With its memorable levels, quirky charm, great presentation, and tons of variety, it remains one of my top games of all time to this day.

Goemon 64/The Legend of the Mystical Ninja.

Goldeneye 007, easily.
And I liked it better than Mario 64 or Ocarina of time. I think one of the things I liked about it over other FPSs was how well it was paced. I’m generally not a fan of dungeon-crawler type games, and most FPSs feel like that. GE007 avoided that, felt more lively and stylish. It had all the style and oomph of a light-gun shooter and all the freedom of movement of a traditional FPS, and it was way ahead of its time, being one of the most influential games in history - while (IMO) being much more fun than many of the games it influenced. Some of its influences include hit zones/head shots (FPSs before this were just bullets and blood, taking as many hits in the head to kill as it did in the foot), and to aid in this - zooming in with sniper rifles - GE007 introduced this too. It also popularized multiplayer console FPS, being the first to have a robust multiplayer mode (a wildly popular one). And it was by far the most successful FPS critically and commercially, at the time of its launch - selling 8 million units and winning the AIAS Game of the Year award, even over Final Fantasy 7 - that is basically the academy awards of gaming, nominated and decided on by the developmental studios of the industry.

Although, since the Wii generation it’s been Ogre Battle Person of Lordly Caliber - given GE007’s lack of availability. The RPG selection on N64 was lacklustre to non-existent, this game was the exception. It’s really well made and fun to play to this very day. There are a lot of notable similarities in the plot with Final Fantasy Tactics - that’s because Yasumi Matsuno began working on this game before leaving for Square and taking his story ideas with him. It’s kind of like how FF7 shares similarities with Xenogears because the initial script was under development by Soraya Saga and Tetsuya Takahashi before they moved to Xenogears. Ogre Battle 64 feels like a bigger game than FFT.

Blast corps was an interesting game too. I always forget about it in the early N64 era. Great pick.

Not the best (though really good and fun), but the first time I actually liked controls in 3D platformer - Rayman 2.

That is one golden 3D plattformer. I prefer the Dreamcast version. Great pick nonetheless. 

Majora's Mask.

True. Shame on me I didn't think of that. Definitely also one of my honorable mentions.