Quite a bit of the fanbase believes that the Happy Mask Salesman's up to something, or is more than he seems. His claim that he was looking for Majora's Mask prior to the events of the game seems kind of suspicious, and he gets quite angry when you fail to return it to him. Granted, he could genuinely want to obtain it to stop it from causing mass destruction, but there's always going to be something fishy about someone so eagerly wanting to get his hands on the local Artifact of Doom. The manga based on the gameshows a more sinister side to him◊.
While most agree that Majora is without a doubt one of Link's most despicable and evil opponents, a large amount of the fanbase sees Majora in a sympathetic light, due to evidence presented in-game that it sees itself as a bullied child.
Some people (like TheStrawhatNO!) theorize that Link is suffering through some kind of mental issues in this game, likely depression.
Some have pointed out that while the people in town seem convinced that Cremia has a thing for Kafei and that he might have run off with her, the dialogue from Cremia and Romani on the subject is actually consistent with Cremia having an unrequited crush on either Kafei... orAnju.
Americans Hate Tingle: The Trope Namer Tingle first appears in this game, though the hate for him hadn't quite reached the level it did with The Wind Waker. At least his map prices were actually reasonable here, compared to The Wind Waker's astronomically high amounts.
Anti-Climax Boss: The final boss, if the Fierce Deity's Mask is used. Even without the Fierce Deity's Mask, the final boss still isn't that difficult. This also holds true in the official manga adaptation of the game. After a lengthy transformation sequence, Fierce Deity Link unceremoniously kills Majora's Wrath in one hit.
The 3DS remake removed Tatl chiding Link for not knowing enemies from Ocarina of Time, which many players found irritating.
The 3DS version also replaces the Suspend Save feature with the ability to make a permanent save, which alleviates the frustration of the time loop mechanic. This save feature can also now be activated on the very first three day cycle.
Guide Dang It! was one of the most common criticisms of the game. The 3DS version includes a Sheikah Stone near the Mask Salesman which you can interact with without any special means. It contains little videos telling how to beat every event of the main quest, plus pictures of every Heart Piece and Stray Fairy in the whole game. The Bombers will also tell you about most side-quests in the game, and they're added to your Notebook as "Rumored events".
Odolwa is considered one of the best and most memorable "first boss" fights in the franchise due to its Dance Battler routine, a strategy that doesn't require you to use the item in its dungeon as became notorious for many post-Ocarina games, its physical design, and its vocals.
Goht for being fought by Goron Link in a fast-paced chase around a circular racetrack.
The Stone Tower Temple, with its unique dungeon flipping gameplay. The level isincredibly difficult, especially if you are trying to find all the Stray Fairies, but it's also considered the best dungeon in the game, if not one of the best dungeons in the series as a whole.
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).
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.
The reuse of assets from Ocarina of Time. Fans either think it was lazy of the developers to not make unique assets or they think it's a vital part of the game's atmosphere.
Ever since a fan-created "trailer" for a proposed Wii U remake made it onto YouTube, fans had 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). It died down when the game was announced for the handheld system.
The changed boss fights in the 3D remake. Some dislike the changes to the fights for their reliance on obvious weak points and changing the flow of the fights, as well as the fact that it renders the Fierce Deity mask less fun to use in that it's impossible to beat two of the bosses with it. Others approve of the changed strategy keeping the fights fresh and find them more challenging.
Although Hyrule Encyclopedia was written by the staff of a fan magazine, admits to taking liberties with Zelda lore, and contains several errors (such as claiming Ganon's reincarnation was all his own doing as opposed to being part of Demise's curse) it posits that Termina is just a creation of Majora's Mask that vanishes shortly after it is defeated. For some fans, this idea is a clever tie-in with The Legend of Zelda: Link's Awakening; others reject this idea as a cruel stab at those who worked so hard to make the land a better place and baseless nonsense that isn't hinted at all in the game.
Contested Sequel: To Ocarina of Time, though on its own the game enjoys a devout fanbase. It doesn't help that the game uses the same assets as its predecessor. 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.
Designated Hero: Majora puts itself into this position, especially when it gives Link the Fierce Deity Mask. As far as Majora is concerned, he's the "good-guy" in this little game and Link is the "villain" who "just runs". Of course, we know who's really the villain here, but Majora is far too childish to see things any other way.
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 (except for the Goron one), 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 Anti-Climax Boss.
Ben Drowned has become one, largely due to Majora's Mask fans growing tired of people referencing the creepypasta every single time the game is discussed. Referring to Link's Elegy of Emptiness statue as "BEN" might even be considered a Fandom Berserk Button. Just read the comments section for the 3DS announcement trailer.
101jacj: 1:17 is not the BEN statue, it is a statue of Link after you play the ocarina song "The Elegy of Emptiness". It is used to create multiple statues that can hold multiple switches down at once. Please like this so the BEN DROWNED morons will stop saying it's Ben.
Theories about the Happy Mask Salesman being evil. While there's still quite a few fans who believe such, there's an equal number of people who are sick of others making him evil just because he creeped them out when they were kids.
The Happy Mask Salesman. He only has a notable role at the start of the game, but his memorable design and quotable lines have made him one of the series' most recognizable characters.
Similar to Dark Link in Ocarina of Time, the Fierce Deity, both characters being the roots of several Epileptic Trees. The latter is seen as one of the most popular incarnations of Link even though he's only an optional powerup for boss levels, thanks to his cool design, overpowered weapon, and mysterious origin. It says something that the fanbase was ecstatic when he was revealed as one of adult Link's palette swaps in the fourth Super Smash Bros. game.
The Skull Kid is a very popular villain in part due to his sad backstory, his trickster personality, the fact that he's one of the very VERY few villains in the franchise as a whole who wasn't Hijacked by Ganon (well, not the Trope Naming one at least), his creepy laugh, and just how cool he looked wearing the titular mask. On that note, Majora's sheer power, horrifying pettiness, and enigmatic backstory have propelled the mask to this status by itself. When Skull Kid showed up in a screenshot promoting the Wii U Smash Bros title, fans were overjoyed until they realized he was only in as an Assist Trophy.
Anju and Kafei. Their sidequest is the most elaborate, long-running, and complex in the entire game, all capped off with a heartwarming resolution. It's practically tradition among players to finish their sidequest before heading off to the Final Boss.
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 theorists include the origins of Majora's Mask (a possible explanation is given in the manga adaptation), the origin of the Fierce Deity's Mask, and the history of the Stone Tower and the Ikana kingdom.
A special case can be argued about the famous line "You've met with a terrible fate, haven't you?". Those eight words have to be the most overanalyzed line in the entire series, with people arguing from whether that line is really directed to Link or to the player, what that "terrible fate" truly means, what does it say about the Happy Mask Salesman sense of morality, or a combination of all of it. Although there are people who think the whole thing is blown out of proportion, particularly because the line is mostly embellished in the localized versionnote In Japanese it roughly just says "You're having a rough time, huh?" (大変な目にあいましたねえ), the fandom at large still goes nuts over it.
Everyone Is Jesus in Purgatory: There's so much worldbuilding and so much sheer artistry that people consider this to be one of the most symbolic games in the entire series. What exactly it symbolizes, on the other hand, is a matter of some debate.
There are some masks that make parts of the game rather easy:
The Blast Mask can be used to produce an explosion in front of Link. It would hurt him, but if you raise your shield as you use it, it somehow blocks the explosion and gives Link a free bomb blast. The only catch is that you have to wait for it to recharge afterwards, you can't use your sword, and you can't target any enemy, although the latter point is rendered moot if you're simply trying to blow up a wall or a boulder.
The Bunny Hood lets Link run around more quickly, allowing him to maneuver around enemies with ease. Couple that with the Great Fairy Sword, and Link becomes a Lightning Bruiser.
The Stone Mask makes Link invisible to most enemies, as they would completely ignore him. This allows him to run past many enemies without getting detected, so he can avoid unnecessary fights. Finding the mask in the first place is a bit difficult at first, but the game becomes easier once you obtain it.
The Fierce Deity's Mask. While it requires 100% Completion to obtain, it obliterates almost every boss, including the final boss.
Chateau Romani. It is a powerful potion that gives Link infinite magic for the rest of the three day cycle after he consumes it. The only catch is that you need to do some side quests to even get to where it is in the first place, then you have to pay two hundred Rupees, and the earliest you can get it is on the first night. However, it can ease the player's worries about ever having to find magic again, which is especially helpful for Zora Link's barrier, the Giant's Mask's magic consumption, or the Fierce Deity's Mask boss slaying magic. In fact, it is best used when you are on the Moon, as no time will pass and you can clear the trials and the final boss without having to worry about finding magic.
There are some very easy ways to get Rupees, some as early as the second cycle where you return to being human:
There are Rupee chests around Clock Town that are refilled with every new cycle, and they are all near East Clock Town. The first just requires you to be human and perform a little bit of jumping to reach. The second requires a bomb near the Bomber's Hideout, which the player can use the Blast Mask for. And the third is only available on the third day on the second floor of the Stock Pot Inn.
The Takkuri is a bird that flies near Milk Road. Upon its defeat, it drops two hundred Rupees, a huge amount that can easily fill up wallets. However, just be careful not to get hit while fighting it, or you will lose a key item and will have to get it back somehow. Wearing the Stone Mask will prevent it from chasing after you, and riding Epona will prevent it from hurting you.
At the entrance hall of Ikana Castle, there are four Redeads that each give up to fifteen to twenty Rupees, and respawn whenever you re-enter the room. They are defeated in one hit by reflecting the sunlight onto them, and will not attack you if you equip any of the three key masks required in Ikana (the Gibdo's Mask, the Garo's Mask, or the Captain's Hat). By wearing one of those masks, they will simply dance hilariously and completely ignore you, making them easy targets. If you take advantage of them, you can fill up a Giant's Wallet in a mere few minutes.
Firing a Light Arrow at a Blue Bubble will destroy it and drop a purple Rupee, worth fifty Rupees. They only show up at night, but they show up in abundance, especially near the Ikana area of Termina Field. They also respawn quickly, so if you just spend a little while around that area and refill your arrows and magic in the many grass patches in Termina Field, you can earn a lot of money.
Dodongos in the Snowhead side of Termina Field during the day. The small one drops practically nothing but the two big ones drop purple Rupees every time. You can then fall in a nearby hole and leave to make them respawn. Said hole also contains two more of the big Dodongos, but they only spawn once per cycle as killing them makes a treasure chest appear.
There is a minigame of sorts in Great Bay where you are challenged to break five pots with a single hit, and the prize is 90 rupees. The trick is to put on the Zora mask, take several steps back, and aim at the central pot. Your boomerangs will break them all before returning to you. The catch is that it's a bit difficult to get the right location for you, and every time you don't succeed, you'll have to pay 10 rupees for the damage you caused. However, you can just give it a go with less than 10 rupees in your wallet, and once you get the right location, you just have to reaim at the central pot after the Zora guy gives you your prize each time. You can get 500 rupees in a matter of seconds with this.
The Great Fairy Sword. It's the game's equivalent to the Biggoron Sword, and while it is not available until late into the game and is rather difficult to get, no enemy or boss will be able to stand in your way once you wield it, although it is a bit unwieldly.
Goron Link becomes this in the 3DS remake. In the original he was powerful but with slow attacks and movement (the goron roll excluded), the remake drastically speeds up his attacks, putting them on par with normal sword swings. These punches do Gilded Sword damage with every hit.
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 Link in the overworld for all three days? It can be done.
The Blast Mask trick. When using the Blast Mask, the explosion is treated as though it were in front of Link, meaning that he won't take damage like he should if he's guarding with the shield.
Despite a "Saving" message appearing when you press start on the title screen after saving at an owl statue, the game doesn't automatically start up your save file, so there's nothing to stop you from saving at the owl statue and copying your save file onto the second slot. This is very helpful if you're playing the Collector's EditionPorting Disaster on the GameCube.
If you save one save slot at the Clock Town owl statue, then load the next slot and save while on Epona at the Milk Road owl statue and reload the first slot, you'll reload riding on Epona while in Clock Town.
The 3DS remake includes a much easier, more convenient way to use the Fierce Deity's Mask outside of boss battles. Granted, there's not much Fierce Deity Link can do outside of battles (he can't open doors without freezing the game, if he can even open them at all, can't use the Ocarina, and his sword beams don't hurt most enemies), but it's still much easier and can be done at any time instead of the last few hours.
In the original game, there's the infinite sword glitch and Bombchu hover. The infinite sword glitch is a holdover from OoT where if you interrupt a stab in the middle of it so the sword keeps its hitbox, which allows Link to run into enemies and deal massive amounts of damage. This also has the side effect making it impossible for Link to fall off of ledges, which leads into the next glitch, Bombchu hover. By backflipping off an edge and quickly pulling out a Bombchu and shielding it, the Bombchu will immediately explode and push Link higher into the air while the infinite sword glitch keeps him from falling back onto the ground. With this, Link can massively Sequence Break to areas he shouldn't be at yet. The best part is, they're both relatively simple to pull off. See it in action here.
Harsher in Hindsight: In this game, Link meets several spirits unable to move to the afterlife, mainly due to Unfinished Business. With his help, they are able to move on and leave behind some of their power in masks. Twilight Princess later reveals that this same Link became a restless spirit following his death, and had to be put to rest by teaching his sword techniques to his descendant.
"No way! No Scrubs!"Explanation What the Bombers say in response to the possibility of a Deku Scrub joining their gang. In today's lingo, it can be taken out of context as the Bombers being textbook "Stop Having Fun" Guys.
A soldier in armor who's so lacking in presence you need the Lens of Truth to see him? Sounds a lot like Kellam from Fire Emblem Awakening, but this game predated it by years.
Zora Link is able to produce a protective electrical barrier when swimming underwater. Then comes Breath of the Wild, which portrays the Zora as being universally weak against electricity, to the point that they seek out help from Hylians because the latter lack this weakness. In fact, touching water in Breath of the Wild (whether by swimming in it or walking in rain) makes electrical attacks deadlier for both Link and his enemies; if Zora Link were to use his barrier in that game, he'd lose all his hearts very quickly as a result.
Dogs being afraid of Goron Link is pretty funny as they can be seen whining in fear and running away. Breath of the Wild inverts this with Daruk, who is so afraid of dogs that when he sees one that he inadvertently saved, he cowers in fear and activates his magic barrier.
Hype Backlash: While the game has received much critical praise and has devoted fans, a number of players dislike the game for various reasons, including the time loop mechanic and the ever-present Guide Dang It!. This has resulted in some frustration over its perceived Sacred Cow status.
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.
The whole franchise started to have this problem with this game, but even after so many entries, the case of Majora's Mask is particularly jarring. 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 everything else, which in turn make a lot of people who don't overlook them to fall straight into They Changed It, Now It Sucks territory.
The 3DS remake is also hit hard but in a different way. You have one camp of fans who decry the remake for merely having "better textures" and otherwise not improving the game's graphics at all, which may stem from the beautifully rendered, fan-made Wii U trailer raising fan expectations too high.note Of course, the notion that it's merely "better textures" is incorrect. Like Ocarina of Time 3D, the 3DS models are much smoother and more detailed than the N64 original. It's just that some models, such as Young Link and Gyorg, are much more obviously improved than other less-obviously improved models, such as the people of Clock Town. On the other hand, you have another camp of fans who denounce the remake for "losing the dark and creepy atmosphere" by improving the colors and lighting, as well as making the Owl Statue save feature, Bomber's Notebook, and Song of Double Time more convenient for players. Additionally, there are frequent complaints over the reworked Zora swimming mechanics, which the original had earned much praise for.
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.
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.
The Goron Elder's son and his crying are an In-Universe example. All the other Gorons in the temple have their hands over their ears, and most of them, when talked to, beg you to do something about the Prince's constant crying before they go crazy.
The high-pitched screams Majora makes during the boss fight will get grating fast.
Hiploops, this game's equivalent of the Helmasaur, constantly make a loud grunting sound when trying to charge at you. This gets especially annoying when one of them can't reach you, as it will continuously make this noise until you get far enough away from it, or hunt it down just to end the aggravation.
The Giant's "singing" during the cutscene after Woodfall Temple where you learn the Oath to Order.
Any mask you're currently wearing most likely will carry over into the cutscenes. This can make certain serious scenes unintentionally hilarious because Link is wearing something like the Bunny Hood during it. Which he most likely will, due to it being very, very useful.
Just before the player fights Gyorg, they get a similar "Jaws" First-Person Perspective moment, which is a Call-Back to when the player fought Morpha in Ocarina's Water Temple. However, it's impossible to take seriously because the player is simply left wondering how the hell Link could not have seen the enormous fish casually swimming a half-circuit around the platform before deciding to attack. With Morpha, it's excusable, because it's about the size of Link's head or a little bigger. Gyorg is the size of a bus.
Throughout most of the nightmarish atmosphere, seeing ReDeads dance is downright hilarious.
Majora's Incarnation's movements, mannerisms, and sounds are so utterly bizarre that they can be hilarious.
The Eels at Pinnacle Rock stop being scary when you have plenty of magic to use for your electric shield—they literally go down in two hits, which is hilariously pathetic for something that looks so imposing.
Painful Rhyme: In the song he sings before he dies, Mikau manages to rhyme "eggs" with "says".
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.
Rescued from the Scrappy Heap: Gyorg and Twinmold's boss fights in the 3DS remake, especially the latter. Their fights have become a little harder but a lot more dynamic, adding extra phases where you fight Gyorg completely underwater and where you fight Twinmold much differently than in the original.
Ron the Death Eater: The Happy Mask Salesman. Many players can't accept the idea that somebody as terrifying as him isn't secretly evil, even if being terrifying was likely unintentional.
Sacred Cow: Along with The Wind Waker, this game seems to have supplanted Ocarina as this within the fandom due to Ocarina suffering from "Seinfeld" Is Unfunny; Majora is hardly hit with the same accusations of being "outdated" as its predecessor due to its Bizarro Episode nature. This doesn't mean it's completely immune from criticism, though.
Resetting time causes you to lose certain items, which means you have get them all over again. This notably includes items for sidequests. Rupees are less of a problem due to the bank... as long as you knew about the bank before wasting too many rupees. Resetting time also means that any progress you made in a sidequest or the main quest can be erased and must be completed all over again if you run out of time (an issue which has deterred optional exploration for some), or if your console accidentally powers off. Fortunately, this trait is a bit less prominent in the 3DS version due to the Suspend Save feature being replaced with the ability to make a permanent save.
In the 3DS remake, swimming as Zora Link has been made easier but much slower. If you want to move at a somewhat decent speed, you have to use the electric barrier attack to move faster, which constantly drains your magic. In an area like the Great Bay, which has no magic refills, this can mean swimming sloooooowly to reach places you want to go if you don't want to use up all your magic, especially if you didn't obtain the magic bar upgrade. You can sort of dash by tapping the shield button, but you only move in short spurts before slowing down.
Also in the 3DS remake, the Bomber's Notebook, while significantly improved, constantly interrupts the game with a slow cut-scene (as opposed to the quick pop-ups of the original) for everything you do. Talk to an NPC for the first time and the book will register them. Complete a side-quest and the book will open up to slowly add that. Fail to fulfill an NPCs request and it'll open up to place a red X saying you failed to keep a promise. This gets more annoying because in the original game the notebook only listed Clock Town residents. In the remake, virtually every NPC you can perform a task for will be added from anywhere in Termina.
Sidetracked by the Gold Saucer: Due to the open and easily resettable nature of the game, players can have more fun messing around than actually trying to save Termina, and there are a lot of ways to mess around in this game:
The first meeting with the Happy Mask Salesman, particularly the Signature Line "You've met with a terrible fate, haven't you?", which created a whole lot of Epileptic Trees just on its own (look above).
The ending of the Anju and Kafei sidequest. By far, one of the most heartwarming moments in the entire series and the perfect ending to what's widely considered, not only the best sidequest in the game, but one of the best sidequests in gaming history.
In the N64 original, Gyorg's introductory cinematic has an attempt at a "freeze frame" effect as the creature dramatically leaps out of the water, during which his name appears onscreen. However, the fact that the splashing water keeps moving well after Gyorg has stopped makes it very obvious that the effect is accomplished by just locking Gyorg's model in place for a few seconds during its jump animation and not actually freezing the image. This was fixed in the 3DS remake, which forgoes the freeze frame in favor of a slow-motion shot wherein Gyorg's model remains animated while his name is onscreen, as well as zooming in the camera enough to prevent any other animations (i.e. the splashing water) from ruining the effect.
The Four Giants showing up to save Termina and subsequently leaving can lose much of the drama when you notice that their feet clip through the scenery as they walk.
King Ikana's head separation attack. It gives him a period of complete invincibility 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.
Majora's Incarnation's Energy Ball attack in the 3DS remake. The only warning for this attack comes when Majora performs a pose, at which point you have only a split second to react before it pelts you with a barrage of energy bolts which not only shaves off a chunk of Link's health, but holds him in place. If you're not careful, this attack will kill you quite quickly.
The first mini boss, Wart, is 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 that you get a lucky shot while it's barrelling towards you at high speed, but you'd better hope you hit it because it's too big to outrun if you miss.
The second mini boss, the Gekko, requires the player to have good reflexes. Otherwise, the player will likely be captured by the massive falling bubble (which is formed every time the Gekko is hurt), which will be very frequent. Whenever that happens, the Gekko will beat Link down like a punching bag, giving no chance for Link to defend himself.
Finally, you have the boss itself, Gyorg. He's big, tough, and he has attacks that absolutely murder poor Link. The quickest way to fight him involves getting in the water with him and buzzing him with Zora Link's electro-shields, which consume a finite and difficult-to-replenish resource in the magic meter and relies on the somewhat-finicky underwater controls. The remake shifts things up by making him easier to hit but also adding a second phase where you're forced to fight him underwater.
Twinmold in the 3DS remake. The boss fight is much harder than their fight in the original version. They do more damage, and you are forced to fight the blue Twinmold without the Giant's Mask while trying to avoid the red Twinmold's attacks. Then you get the Giant's Mask, and the second phase begins. Rather than slash away at it with your sword like in the original game, you are now required to wail on the red Twinmold with some rather slow attacks in order to stun it. Even if you got the upgrade from Great Bay that halves damage and several heart containers, this fight can eat through your entire life bar if you don't know what you're doing. They're also immune to the Fierce Deity's Mask, so you have to fight them the hard way.
The Goron trial on the Moon. It's a Goron-roll track section involving tight, narrow bends, and half of which revolves around a mechanic where you have to ricochet off chests in precise ways in order to make 90-degree straight turns. You need an extremely steady hand to get it right. It becomes infinitely easier if you don't actually touch the control stick and just let the chests ricochet you around, but even then it can be supremely disorienting and requires precise initial aim and timing of when to stop.
The Zora trial on the Moon in the 3DS remake. Instead of being a simple underwater maze, the mini-level has been altered so you have to hit a switch, rush through the pipes, find the barely visible fish that mark the correct path, and manage to make a perfect dolphin-jump out of the water to reach the next room before the gate closes. Miss the hard-to-make jump? It's all the way back to the beginning for you. One of the Heart Pieces specifically requires going through a wrong path which is marked only by a single pot.
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 their skills. The Deku Playground game, the two Target Shooting galleries, and the various Deku, Goron, and Zora racing games are examples of this.
Obtaining all the stray fairies, especially in Snowhead Temple and Stone Tower Temple, can be incredibly frustrating. Snowhead Temple has numerous invisible fairies and one that requires you to use Deku Link and float sloooooowly down for about three minutes to reach, and Stone Tower Temple has some that require doing something deep in the temple, going outside to invert it, and then going all the way back through to reach the chest containing the fairy.
The moon, which has a very weird and overall creepy looking face on it. The 3D remaster manages to take it Up to Eleven by exaggerating the creepiness of the face a bit.
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 them, but especially Link's.
Goht has an eerily human-like face, considering that the monster itself is a huge mechanical bull/goat.
The Great Faeries, just like in the last game.
At least one reviewer has noted how the updated graphics in the 3D version somehow make them even creepier.
Underused Game Mechanic: The majority of the masks in the game suffer from squandered potential, as many of them are good for exactly one little thing and then have no more use except for obtaining the Fierce Deity's Mask.
Unintentionally Unsympathetic: Skull Kid. You are expected to pity him for being posessed, even though the whole plot could have been avoided if he didn't steal from the Happy Mask Salesman.
Vindicated by History: The game had some negative reception in its time, being a sequel to an incredibly beloved game, and it sold a lower number of copies than Ocarina of Time. The latter situation wasn't helped by it being a late N64 title and the fact that the North American version came out the same day as the North American release of the PlayStation 2. Years later, it's achieved a decent amount of popularity for its incredibly frightening and bleak atmosphere, having a dungeon that is considered one of the best in the series, 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 2000-2009 Game of the Decade list.
The Deku Scrub 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 (or at least, Goron Link can't). It's no wonder no one took him up on his offer before you did. Then there's the Deku Scrub 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. And then there's the one in the southern swamp, who sells magic beans only to Deku Scrubs, who are, like Gorons with bombs, incapable of using them.
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.
The player has the option to make Link himself into one. Upon entering Ikana Canyon during the day, the player can see Sakon the thief running around and has the option to talk to him. Despite it being very obvious by this point that Sakon is unscrupulous, untrustworthy, and steals anything he can get his hands on, the game gives the player the choice to agree to loan him Link's sword when Sakon asks for it. Fortunately, if the player chooses "Yes", they're spared having the sword stolen by Tatl flying in Sakon's face and scaring him away.
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.