Eh, as anyone who's read my post in this forum would probably know, I'm a huge Legend of Zelda junkie, so it probably shouldn't be a surprise that it's an LoZ game that's my favourite. And I already stated which my favourite Zelda game was in another thread, so I guess I'll just repeat out from that.
Majora's Mask is my favourite game of all time (at least so far :p), and probably will continue to be for a while, unless Nintendo manage to bring something truly amazing out with the Wii U. Despite thinking it was only a demo at first, and being stuck for a long, looong time, because I had so much trouble with just the first area, it eventually came to be my favourite game of the franchise. I'm actually pretty proud that I managed to get all masks on my own, without any help, because I often find myself guilty of using a walkthrough whenever I get stuck, so when I look back at all my old games and find that I've actually beaten or gotten far in so many of them, I get kinda surprised :p But yeah, I revisited the game quite a few years back, and noticed a lot more details that I'd never noticed before.
So basically, back when I first played through it, I didn't really pay attention to the whole message of the game, I wasn't quite as drawn by the dark atmosphere of the game, and all in all, I only cared about beating it, but that was mostly due to the fact that I didn't understand a single thing in the game. Playing through it again, learning of exactly what was happening and realising all the small details of the game, it's certainly been one of the most captivating games. Unlike Ocarina of Time which seemed to focus more on the gameplay, this game focused mainly on the environmental details, the atmosphere, and basically capturing the player in all of this, and it actually made me enjoy the game even more. Being under a time constraint, and constantly feeling how the end of the world got closer and closer with each minute that passed, and how the moon grew bigger and bigger with each day. It's just.. they just did everything right in that regard.
The gameplay was also superb, but then again, it was essentially just a copy of Ocarina of Time when it came to the gameplay, so no wonder :p But I really liked the dungeon designs of this game, all the sidequests were mostly enjoyable, and the transformation masks omgggggggggmmgjfsdfhdhf. I just loved rolling around as a Goron, swimming around as a Zero, and... nah, being a Deku Scrub wasn't quite as enjoyable as the others, but I just really liked the idea, and how it was used in the leading quests that gave you access to the dungeons, and how it felt like each mask gave you so much more to do. Yet another thing they got right. And the use of the internal clock to incorporate the 3 days system- one of the things that made the game as awesome as it is. And while I did find it to be annoying at times, because it forced me to be on schedule with things AND THAT'S ONE THING I'M HORRIBLE AT, it definitely didn't make it any less awesome. And for what I've heard, it was initially supposed 7 days, which I would've loved to see, but I think it'd be kinda tedious, since it'd probably mean a lot of waiting around for certain events. But still, it'd mean there'd be so much more to do in the game. But since they only had one year to make the game, I'm glad they settled for 3 days, because I feel like it would've significantly lowered the quality of the game, if they tried to put too much into it with too little time, instead of just polishing whatever they had. But yeah!
There's not much to say about the story honestly, because most of the game is actually side-quests, which each bring out their own little stories. But the general story is:
A lonely Skull Kid gets possessed by Majora's Mask, after he tried wearing it. The mask uses him in dooming Termina, by having the moon crash down into the Clock Tower after 3 days. You arrive in Termina in a search for "an old friend", presumably Navi. As always, you have to save the day, this time by making your way through 4 temples, to acquire the help of 4 giants, to stop the moon from crashing into the Earth. Afterwards you go beat up the Mask.
Yeah, not that much story over it really, but again, with all of what the general atmosphere of the game, the gameplay and the side-quests bring you, the story isn't really that necessary for the game to still be great, and what we have is quite enough.
But yeah, I think I've tl;dr'ed enough, and even if it may not still be clear to why it's my favourite game, it's just a personal preference. Some may enjoy the story of Ocarina of Time more, or the gameplay of Skyward Sword more, but I just feel like the atmosphere that Majora's Mask brings is really a good selling point, and combining that with everything else the game offers, it's just amazing. I know that Twilight Princess tried to bring forth the same dark feeling, but it just felt kinda forced, where as in MM it was kinda subtle, and as I said, I didn't really notice it as a kid, which just made it all the more surprising :p