I want to highlight a few noteworthy mods (because this question will come up eventually :-) ):
Super Mario 64_
- Mario Builder 64: A Mario Maker like editor build into the game engine itself. There are many user created levels you can download and play. Probably my favorite Super Mario 64 Romhack. The only problem is, that saving is not possible and user created levels cannot be imported in a normal emulator (as far as I know). For all the extra features you need a special setup. Read more at https://rentry.co/MB64-Setup-Guide . Also due to a DMCA by Nintendo, this Romhack is banned from romhacking.com
- Shotgun Mario 64: Exactly what it sounds like; you have a shotgun and can shoot.
- Land: A classic styled linear progression with new levels and power-ups, inspired by Super Mario 3D Land and 3D World.
- Movement Mastery / Madness: Series of short challenges with time tracking, to practice and master movements.
- The Green Stars: A full new Mario 64 adventure with 130 stars and a Galaxy aestetic. Has lot of QoL improvements.
Zelda OoT_
- The Missing Link: Mini adventure that plays between Ocarina of Time and Majora's Mask. Link is on his quest to find Navi.
- Star Fox 64 Survival: A crossover from Star Fox! You play as Fox and need to survive the unknown planet.
- Sealed Palace: A popular and extensive Romhack. I didn't play it myself, so not sure how extensive it is. It has custom cutscenes, songs, 100 Skulls and 20 hears to collect.
- Cystal Clocks: 11 puzzle rooms with platforms and crystal activations. Puzzles are mostly time-based. Shoot with a modified slingshot mechanic.
Mario Kart 64_
- Amped Up: 16 new courses, new game modes, music, graphics and gameplay techniques. A brand new Mario Kart game... sort of.
- Hooting Time: Lots of new options, 16 characters, new game modes, randomizing options and lots of more.
F-Zero X_
- Climax: Changes graphics and tracks based on the Japan only GBA game with same name.
- Unlocked: Simply unlock all pilots, modes and courses. Also gives infinite lives.
Banjo Kazooie_
- The Legend of Banjo-Kazooie - The Jiggies of Time: A complete new Banjo adventure in the world of Zelda. Has 9 worlds, 100 jiggies, 900 notes and 5 mumbo transformations!
Conkers Bad Fur Day_
- Uncensored: I actually don't know the details of what is uncensored, but here it is. Something must be uncensored I guess. :D