Not only is Majora's Mask my favourite Zelda title, it's my all-time favourite game. For so many reasons, some of which I can't even pinpoint.
Firstly the many tropes within the game; from the positive aspects of friendship, forgiveness, to the negative of death, despair, etc. The game has a massive amount of emotional value to the game. Not only are there emotional story arcs around the central characters, (The Deku Butler, Darmani, Mikau) but many of the background characters also - (Grog, Kamaro, Anju/Kafei, The Townspeople).
The character mirroring/duplication was a really clever concept, although some people see it as being lazy game design. Like the Happy Mask Salesman being a psychotic weirdo, Koume and Kotake being good guys, the "sell me something with c" character as a banker, I think that it's all ingenious!
Moreso, the gameplay - it improved vastly on what Ocarina of Time had started, but unfortunately will never step out of it's shadow. The controls, the graphics, the depth. Link, being more agile, reacting differently with different masks, etc. Plus the enemies were a lot more difficult, skulltulas provided more of a challenge, in that they turned more frequently, lizalfos were more difficult to fight, etc.
The dungeon designs are challenging, but getting to them is even more so. A nice addition was the option to battle the bosses again, something Ocarina lacked. The rewards from playing the game are so, so satisfying. I can say the same for the collectibles - Fairies, Masks, Skulltulas.
The visuals in some places are really trippy and intense, (inside the astral observatory, fighting Odolwa, and of course fighting Majora)
The final thing I love about the game is the "doom and gloom" of it. The morbidity of the whole thing. You have to ease so many people's suffering, there's a freaking MOON about to land on Termina, while everyone in Clock Town just waits and accepts it. Plus, there's a canyon of death filled with stalfos, gibdos, invisible ninjas, etc.... Ikana, basically. One of the most challenging, and definitely the most Interesting area in Zelda that I can think of.
I <3 MM. So much.