These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Quite a bit of the fanbase seems to think the Happy Mask Salesman's up to something, or is more than he seems...
While most agree that Majora is without a doubt one of Link's most despicable and evil opponents, a large amount of the fanbase has Majora seen in a sympathetic light, due to evidence presented in game that it sees itself as a bullied child.
Applicability: The game is often believed to be an allegory for death, but so many elements of it, separation, loneliness, and Link's own history either are examined or can be inferred from it that the player can draw several of their own conclusions from the game's stories and symbolism. Observe.
The Beaver Brothers that live on top of the waterfall near Zora's Cape. If you go see them, you can play a swimming mini-game for a bottle and a piece of heart. They have no actual bearing on the plot whatsoever, and outside of the completely optional mini-game (which you have to search out yourself), they never show up elsewhere in the game. Keep in mind, THIS is what they look like (and the little brother's eyes and circle on his belly also spin and light up like a Christmas tree).
Being this the first Zelda game that stars Tingle, even at his age of 35 he still has the mind of a child, believing in fairies and even dressing like a Kokiri.
The hand that lives inside the toilet at the inn. Even in the face of Tingle and the Beaver Brothers, that's just weird.
The Aliens. Though they do get foreshadowed before their actual appearance, the fact that there are aliens in a Zelda game who steal cows and apparently lobotomize a young girl is pretty jarring.
Broken Base: Ever since a fan-created "trailer" for a proposed Wii U remake made it onto YouTube, fans have started to argue whether Majora's Mask should be remade for the 3DS (to logically follow up on Ocarina of Time 3D) or for the Wii U (for prettier graphics).
Contested Sequel: To Ocarina of Time, though on its own the game enjoys a devout fanbase. There are fans who love the sequel's emphasis on sidequests, the time limit and the twists on the series' formula. There are fans who prefer Ocarina of Time for its more traditional approach in terms of story and gameplay, as well as its bigger influence and impact on the gaming industry. There are fans who like both games alike, too.
Disappointing Last Level: Players expecting a large-scale final dungeon will be disappointed, first because the dungeon segments in the Moon are brief and only require some basic skills from the mask transformations, and second because they're not even required to reach the Final Boss. In fact, completing them by trading all masks will lead to getting the Fierce Deity's Mask, which will turn the final boss into an Anticlimax Boss.
Epileptic Trees: This game has been a goldmine of kooky fan theories, mainly because it takes place in a parallel dimension without much history or backstory. Fodder for theorisers include the origins of Majora's Mask (a possible explanation is given in the manga adaptation), the origin of the Fierce Deity Mask, and the history of the Stone Tower and the Ikana kingdom.
Fountain of Memes: Due to the Mayan calendar supposedly stated for the End Of The World in December 21, 2012, you'll see a ridiculous amounts of the "Dawn of the ___ (being 48, 24 and Final Day)", and an out of universe character's reaction to the date. The game is also the key element of the Ben Drowned creepypasta, which took many of the lines in the game and gave them a sinister context that proved popular with the audience.
The Stone Mask in general makes much of the game's challenge evaporate, as most enemies will ignore Link when he has it on. Fittingly, finding the mask in the first place is a bit of a Guide Dang It but laughably easy once you know where to find it.
Chateau Romani, which gives you infinite magic for the entirety of the current loop after consumption. The only catch is that you can only get one on the night of the first day after doing a few quests. Combine with Zora Mask for infinite electro-barrier, Giant Mask to make the fight against Twinmold a lot easier or Fierce Deity Mask for effortless boss pwnage. It gets even better when you're on the Moon — since there isn't any time there, Chateau Romani lasts for as long as you're up there. So you can go through the whole dungeon with unlimited magic (which makes the boss fight even easier).
At the entrance hall of Ikana Castle, there are 4 Redeads that each give up 15-20 rupees and also respawn whenever you reenter the room. They're also one-hit killed by the sunlight once it comes into the room, and just plain trivialized by an item you naturally have at that point. By abusing the Redeads, you can easily get 500 rupees within a single game hour. Not to mention that some masks will cause them to dance and completely ignore you, making them easy targets. Before you get to Ikana, the Dodongos in Termina Field are a good source of Rupees. The two larger ones drop 50 and the smallest one typically drops 15-20. They're only out during the day though.
There are 100-Rupee chests around Clock Town that are refilled with every new cycle. One of them is only available on the Third Day, but you can get two of them right away.
The Takkuri, a bird that, if defeated, earns you a whopping 200 rupees in one shot, which happens to be just enough for the Chateau Romani (once you unlock it initially). Of course, if the bird lands so much as a hit on you, it can steal one of your key items, so there is a risk involved — unless you use the Stone Mask or Epona while fighting it, as you are invincible on the horse and the bird will ignore you even as you shoot it to death with the mask on.
Using the Blast Mask while you raise your shield blocks the explosion damage, which basically means you have infinite bombs and have no need to collect regular bombs.
The Bunny Hood lets you literally run circles around your foes, making you move twice as fast. Combining it with the Great Fairy Sword turns you into a bona-fide Lightning Bruiser.
In Sakon's Hideout, when you're switching places with Kafei in order to grab the Sun Mask, by wearing a mask as Link, switching to Kafei, then swapping the mask Link is wearing with another mask (normally not allowed), Link will automatically put on that mask when you switch back, even if it's a mask that you shouldn't be able to use. The Giant's Mask just freezes the game, but the Fierce Deity's mask...
In a bizarre, yet totally legitimate (i.e. not requiring cheat devices) glitch, it is possible to enter Sakon's hideout earlier than you're supposed to, by running at the precise angle toward the crack between the right side of his hidden door and the wall, and rolling the moment before you hit it (or just running into it for several seconds). You have to get the angle and the timing perfectly. Fierce Deity in the overworld for all three days? It can be done.
The Blast Mask can be used as a source for infinite bombs by simply raising your shield when the mask is used. The game is programmed to block damage to Link if the source of damage is in his front and his shield is raised. Since the mask's explosion is technically in front of Link, the shield can block it.
Hell Is That Noise: If you go into the clock tower on night of the last day (required to complete the prologue), Skull Kid demonstrates the power of Majora's Mask by screaming at the top of his lungs, thus bringing the moon down even faster and the battle BGM starts off with a frickin' scare chord. No points for guessing where the two tropes lead. The mask salesman's laugh also qualifies.
I Am Not Shazam: Many are under the impression that the Skull Kid's name is Majora. He's simply the guy who stole the mask from the Happy Mask Salesman.
It's the Same, so It Sucks/They Changed It, Now It Sucks: The whole franchise started to have this double standard problem with this game, but even after so many entries, the case of Majora's Mask is particularly jarring. Basically, the "It's the same" problem comes from how the game recycled many graphic assets from Ocarina of Time, which makes it look very similar quite often, and thus alienating some people to overlook the differences in... well... pretty much everything else! Which ironically make a lot of people who don't overlook them to fall straight into the "They changed it" territory.
Jerkass Woobie: Skull Kid. His pranks frequently cross the line between a fun joke and an unfunny one, but he does it because he has hardly any friends, and because the mask he's wearing is gradually taking control of his actions anyway.
Moe: Romani, mostly because of her cheerful personality despite her concerns regarding the ghosts that attempt to take away the cows. Her model being based on that of young-age Malon in Ocarina of Time helps as well.
Most Annoying Sound: The Goron elder's son and his crying. All the other Gorons in the temple have their hands over their ears, and most when talked to beg you to do something about the Prince's constant crying before they go crazy.
Nightmare Retardant: Throughout most of the nightmarish atmosphere, seeing ReDeads dance is downright hilarious.
Player Punch: Take your pick. Nothing like seeing your favorite Ocarina of Time characters crying into their hands as their life is in tatters with the end of the world nigh to make you realize how deeply attached you are to them.
Scrappy Mechanic: Resetting time causes you to lose certain items, though rupees it's a less of a problem due to the bank, but it does mean you have get them all over again. This notably includes items for sidequests.
The end to Anju and Kafei's sidequest is the most touching moment in the game, and definitely the sweetest... or at least it would be, if Tatl didn't have to go and point out that "even though they're lovers, they look just like a mother and child."
The mysterious hand that lives inside a toilet at the Stock Pot Inn.
That One Attack: King Ikana's head separation attack falls under here. It gives him a period of complete invincibilty until it's over, and Link will only be able to target his head, leaving him exposed to the body's sword attacks. The head will then latch onto Link in an unavoidable bite and hold him in place while the body slashes at him. Ikana will use this attack more often as he takes damage, drawing out the fight.
Gyorg. His big, he's tough, he has attacks that absolutely murder poor Link, and the quickest way to fight him involves getting in the water with him and buzzing him with Zora Link's electro-shields.
And for minibosses, there's Wart. A huge eyeball completely enveloped by smaller eyes that must be disposed of before you can damage it. You can use your bow and hope for a lucky shot while it's barrelling toward you at high speed, but you'd better damn well hit it because it's too big to outrun if you miss. Oh, and there's two of them you have to deal with in the dungeon.
The Great Bay Temple can be considered even harder than Ocarina of Time's Water Temple. While the puzzles aren't as confusing, the currents in the water makes navigating it very frustrating, and both minibosses and the main boss are infamously hard.
Anju and Kafei. Not only does the quest involve a lot of waiting around and running back and forth to get to specific locations at very narrow periods of time, you have to do it twice to get all the rewards. And it's very easy to mess up a step and have to start over.
Some of the minigames can be exceptionally difficult if the player doesn't hone his/her skills. The Deku Playground game, the two Target Shooting galleries, and the various Deku, Goron and Zora racing games are examples of this.
They Just Didn't Care: The Zelda Collector's Edition. The audio glitches up horribly whenever you travel from one area of Clock Town to another. The game crashes randomly and without warning, wiping off all of your three-day-cycle progress. Even worse, they actually included a start-up screen practically apologizing for any audio discrepancies you can't help but notice.
Ugly Cute: The Skull Kid when he's not wearing Majora's Mask. It helps that, as Tatl's flashbacks show, he was quite The Woobie.
Majora's Incarnation. Its squeaky "voice" and weird dances doesn't help for that matter. Majora's Wrath to a lesser extent. The Happy Mask Salesman, too.
The Elegy of Emptiness statues... all four of 'em, but especially Link's.
The Happy Mask Salesman, even more so than in the last game.
Vindicated by History: The game had some negative reception in its time, being a sequel to an incredibly beloved game. Years later, it's achieved a decent amount of popularity for incrediblyfrightening and bleak atmosphere, the dungeon designs being some of the best in the series (although they are pretty damn hard), the huge amount of sidequests, a wide variety of interesting items, and more. All in all, it's a lot more popular than it was originally, to the point Gamefaqs even made it Number 1 on the the 2000-2009 Game of the Decade list! To some, it even surpasses its predecessor and it's routinely discussed as one of the best Zelda games and games in general.
The Deku Nut salesman in the mountains offers you a trade: you give him your Big Bomb Bag and 200 rupees, and he gives you a Biggest Bomb Bag. Here's the thing, though: He sells only to Gorons. Gorons can't use regular bombs. It's no wonder no one took him up on his offer before you did. Then there's the Deku Nut Salesman who sets up shop inside of one of the Indigo-gos rooms. And the only ones that can even go in there are the Indigo-gos. That's a five member client base he's selling to. Even worse is that he's set up inside Lulu's room. Lulu being the only female member of the band. Now, Zoras might not see any need for gender privacy, but if they do, he's limited to Lulu and Mikau most of the time.
The Clock Town Banker, for stamping your bank balance on your forehead. As the Versus guide points out, he deserves to be defrauded for that.
What Do You Mean, It's for Kids?: Druggy and nightmarish visuals and cinematography; death and hopelessness permeates every quest and every second of gameplay; has some of the most legitimately frightening moments in Zelda history; and that's just the first hour. If the game were released today it'd be an E10+ at least.