Majora's Mask is the best Zelda game of all time.
First off, it was a bold experiment in storytelling. The three day cycle was innovative and interesting, as it really showed that things happen all the time without us even knowing. It's really amazing, the amount of sidequests and NPCs there are, and how one event can really lead to another. In just one example of how changing one event can change history, to get one of the special masks you had to rescue the woman who owns the bomb shop from a thief. However, if you stop the thief, he won't reveal the location of his hideout and that will prevent you from doing another quest. However, it's not like the other quest is lost forever, because you can just go back to the Dawn of the First Day and do something different.
Second, the game has incredible atmosphere. In the world of Termina, everything is just a little off. From the bell tolling to the occasional earthquake due to the moon coming slowly closer and closer, the game oozes character. There are little touches that make the game so worth playing and paying attention to. It is also a lot darker than Ocarina of Time, with frank talks of death and the constant sense of impending doom that pervades the game and every NPC in it.
Third, the puzzles and dungeons are downright brilliant. there are only four dungeons, fewer than any other Zelda game I believe, but they are massive. The Great Bay Temple makes the Water Temple jealous - and I mean this in the most hair-pullingly awesome way. The Stone Tower is one of the greatest Zelda dungeons of all time, as voted by pretty much everyone who's voted on such a poll. The puzzles, the twisting and turning, and the excellent music makes it one of the most memorable places in a Zelda game.
Fourth, there is just so much to
do! Seriously, the amount of sidequests to do, the amount of people to help, and the places to explore alone put it as a game that will last you hours upon hours, but when you factor in the main story and dungeons you have one of the longest games on the N64. There's no wonder it needed the Expansion Pack to fit it all in!
Finally, I want to rebut a few points made by Dagger.
I hated Majora's Mask. Worst Zelda game by far.
I'm assuming you've never heard of The Faces of Evil or The Wand of Gamelon, two mediocre-at-best Zelda games for the CDI with abominable cutscenes and voice acting. As long as they exist, there is no way any other Zelda game can be considered the worst.
Majora's Mask had the ANNOYING issue of erasing the events every time you had to reset time. When I complete a task, I'd like the dang thing to STAY COMPLETED.
Well, of course! You see, Dagger, when you go back in time, things you've done don't stay done. That'd be silly. Besides, the only things reversed are your sidequests, as you get to keep any masks or heart containers received via sidequests, and any dungeon you have completed stays completed in that all doors are unlocked and you still have the remains of the bosses that you have defeated (which are necessary to access the final dungeon and fight the final boss). You don't lose masks. you don't have to complete a dungeon again. You don't have to get a heart container you already got. you don't have to re-upgrade your sword. The only thing changed is the status of the NPCs.
It's a really simple concept with brilliant execution.
Also.... Majora's Mask introduced us to the absolute most worthless abomination to ever show up in a video game:
Do you really want to vote for the game that gave us THAT guy? I'm just saying. Think before you vote.
And I'm saying, why let such a minor part of a game make you vote for something completely different? Tingle has about five minutes of screentime in Majora's Mask and it's all optional. You shoot down his balloon, buy a map, and then you leave. What's wrong with him, anyway? Why the hate? I happen to think he's funny!
In conclusion, Majora's Mask did everything right. It gave us innovation. It gave us puzzles. It gave us atmosphere, story, music, and brilliant level design. But most of all, it improved on Ocarina of Time. Instead of trying to best its famous predecessor, Majora's Mask took the series in a radical but familiar direction with new gameplay mechanics out the wazoo. It is hands down my favorite Zelda game ever and for good reason: In a series full of brilliant video games, Majora's Mask hit all the right notes and it did while pulling off something new.