Majora's Mask is by far my favorite Zelda game to do 100%. I've started runs of the game actively trying to not do 100% many times and ended up doing 100%. The two games I rank above Majora's Mask overall are much less enjoyable for me to do 100%. Ocarina of Time I usually do about 90% of the game as I pick and choose the side content I enjoy to complete (I hate fishing and the Simon Says ocarina game), but I've completed it 100% maybe 10 times. Breath of the Wild I've never completed 100%, and I don't think I ever want to do that.
Majora's Mask just has fantastic side content that is as enjoyable as the handful of dungeons that it has. Another factor is the length of the game. Majora's Mask has relatively few annoying quests because there's just less content than the other 3d games and that actually helps in wanting to do 100%.
Favorite games overall from my signature:
1. Ocarina of Time 2. Breath of the Wild 3. Majora's Mask 4. A Link to the Past 5. Wind Waker 6. A Link Between Worlds 7. Skyward Sword 8. Twilight Princess 9. Link's Awakening 10. Phantom Hourglass 11. Adventure of Link 12. Legend of Zelda 13. Minish Cap 14. Oracle of Ages 15. Spirit Tracks 16. Oracle of Seasons
Favorite games to do 100% ranking Wind Waker separately for with and without figurines:
Love
1. Majora's Mask - couldn't imagine not completing 100%
Enjoy
2. Wind Waker minus figurines - Great side content and great game overall.
3. Legend of Zelda - very little to collect and finding everything makes the game easier and for me more enjoyable.
4. Adventure of Link - very little to collect and finding everything makes the game easier and for me more enjoyable.
Like but strongly prefer to do less than 100%
5. Twilight Princess - nothing super tedious in the side content in my opinion besides the Cave of Ordeals and a good game overall.
6. Ocarina of Time - a handful of annoying minigames or side content that I usually skip when playing the game. Definitely my favorite game overall though and have played the most.
7. Skyward Sword - a little more annoying side content than Twilight Princess, and the harp minigame actually prevented me from doing 100% until the HD release.
8. A Link Between Worlds - great game, but I remember a handful of annoying side quests that I don't enjoy.
9. A Link to the Past - I've rarely completed 100% simply because this is the only game I regularly play that I struggle to remember where to find everything.
10. Link's Awakening - the remake actually is worse to 100% because of the chamber dungeons.
Haven't completed 100% but would like to do that someday
11. Phantom Hourglass - I enjoy this game, but I have never found everything.
Would never want to complete 100%
12 (tie). Breath of the Wild - I actually tried once to find every Korok seed, found around 500, and vowed to never try again.
12 (tie). Wind Waker - I would never want to try to find every figurine.
12 (tie). Minish Cap - I wouldn't mind trying to do everything but the figurines, but the figurines are unbelievably tedious.
12 (tie). Oracle of Ages - I didn't like the ring system and far from my favorite Zelda game.
12 (tie). Spirit Tracks - has some good side content, but I would never want to do it all.
12 (tie). Oracle of Seasons - my least favorite Zelda game I've played, and I didn't like the ring system.