Level 6. Being the first appearance of the Wizzrobe enemy, and also swarming with shield-eating Like Likes and paralyzing Bubbles.
Zelda II: The Adventure of Link
Death Mountain. It's filled with obnoxiously hard enemies (even by this game's standards), and is an extremely confusing maze.
The Great Palace is plagued with completely unconventional mechanics compared to the rest of the game, including horrid dead-ends, endless loops, and monsters with increased hitpoints relative to what they have when encountered elsewhere.
A Link To The Past
The Ice Palace can become seizure-inducing due to the tougher bestiary, obstacles and maze-like layout. In particular, there is a switch in B6 which requires hitting a red/blue switch, then doubling back several floors in order to push a block down from B5 onto the switch. Luckily, having the Cane of Somaria makes it much easier. note In fact, until the Updated Re-release, it was almost assumed that any player would do the dungeons out of order so that they could tackle the Ice Palace with the Cane of Somaria. When your dungeon is so hard it drives normal players to Sequence Breaking, you've definitely got a Scrappy Level on your hands. Worse, the map is rendered pretty much useless due to most rooms being made up of discrete sections. Nothing worse than finally getting halfway down correctly, then remembering that warping to the beginning of the level flipped the red/blue switches.
Turtle Rock's confusing floating platform track sections. Particularly the first one, which forces you to ride through four lamps, shooting each of them with the Fire Rod to light them all and open the door, THEN run back and get through the door before one of the lamps goes out and it closes. "Don't go any further without a green potion" indeed.
Catfish's Maw, where a miniboss steals the dungeon item and requires you to pursue it all over the damned dungeon to its hidey-holes. The last one is extremely difficult to find, as it is very close to the entrance in an area the player has likely long since visited and won't think to go back to.
Link's Awakening's Turtle Rock, the last main story dungeon, is an absurdly complicated and massive maze where every previous miniboss from the game appears as respawning enemies; the dungeon's unique miniboss is capable of knocking Link back to the dungeon entrance; one puzzle requires Link to shoot an arrow into the eye of a random statue (while this is normally a Zelda staple, this is the only time in the game this is required, and it occurs in the eighth dungeon); and, completing the dungeon requires the player to visit a hidden room whose entrances are not even on the Dungeon Map.
Ocarina of Time
The Water Temple is, by far, the most infamous dungeon of the game, if not the entire series. It probably says something that in the Master Quest mode of the 3DS remake, which upped the difficulty of the dungeons enormously, the Water Temple inexplicably became easier. In fact, Ocarina's director has officially apologized for the Water Temple. This was fixed in the 3DS version, where both types of boots are considered as items rather than equipment, and can thus be mapped to a shortcut button. Also, the paths leading to the altars to change the water levels have lines leading to them which are Colour-Coded For Your Convenience.
The main reason for the Water Temple being so hard is because of the fact that after some time exploring the temple, you will get a key that must go to a certain door, but this door is not the first locked door that you encounter and you will undoubtedly use the key on the wrong door. If you do mess up, it takes much longer.note One very persistent rumor is that it's possible to use the keys in the wrong order, and fail the whole temple. That's right, many players still believe you can actually permanently screw up the Water Temple. And what does that mean? Restart your file! To be fair, you can get into situations where it seems like this is the case — you can actually still solve it if you take the right course of action, but if you can't manage to find that action, it seems like you're stuck forever. As if it weren't bad enough, it's possible to miss the item that makes it nearly tolerable. That's right: somebody did the whole Water Temple without theblue tunic. Another reason is the miniboss Dark Link, which due to a quirk of programming, takes much less time to beat on a three-heart run.
The key in question is most likely the one in the basement area of the temple's central pillar/tower-like structure. In a vertical area filled with spikes, narrow walkways and floating platforms, the natural thing is to go up, riding the floating platforms as you make the water level rise. It's not at all apparent that the player must then jump back into the water and swim down into the nest of spikes, which will reveal a hole that was previously blocked and obscured by the previously mentioned floating platform. Finding this key makes the temple significantly easier, and since the player always seems to be missing just one damn key, the shortage of keys situation is far less likely to happen when this area is fully investigated.
Jabu Jabu's Stomach was no slouch either. Almost all enemies will electrocute you if you attack them, so most of them are either very difficult to bring down or outright unkillable until you get the boomerang.note The Zora princess herself can be thrown at the jellyfish, bubbles etc to kill them with little risk to you. When thrown, she giggles; she's immune to damage. One of the few times you can directly use an NPC *as a weapon*, and she seems to enjoy the experience. You can also make the jellyfish safe to kill by stunning them with those Deku Nuts you almost never use. And also the Zora princess yells at you if you leave her, even though under certain circumstances, she'll vanish all on her own.
The Ice Cavern. It's frozen water. And horrible. The constant falling icicles are annoying, and so are the ice monster ... things; but the level can be done fairly quickly if you know the right route, and the wolf at the end is an Anticlimax Boss.
The OOT expansion Master Quest turns most of the dungeons into this, but the Fire Temple will probably make you prematurely finish your game if you've come this far. Irritating use of fire, frequent use of lighting torches by firing arrows in front of them (to the point where it's better to beat the Water Temple first and get the Fire Arrows), maze-like layout, and probably one of the most frustrating puzzles in the series. This puzzle involves trying to get to a key by pushing a switch, quickly running to a hookshot target, and trying to get to the chest before the fire rises. Thing is, the switch has an improbably short fuse, so unless you learned the scarecrow's song, good luck.
The Bottom of The Well. First off, if you even want to get into the place itself, you need to walk through a wall. That's right, you need to go through an unassuming, totally generic looking wall that has no special markings on it, and the only hint you get is Navi telling you to "see the truth." But the fun doesn't stop there; the dungeon is filled with fake floors, which drop you into a cavern filled with redeads. Like the wall, these parts of the floor aren't marked in any way, so you need either a walkthrough or lots of trial and error to get past certain areas.
The Great Bay Temple features a complicated series of switches, currents, waterfalls that must be frozen and thawed, etc. The crowning evil of this dungeon would be that in the second room there are three switches. Pressing the wrong ones reverses the current in the entire level, making it impossible for you to proceed until you return to hit them again. Also of note is the fact that almost the entire level is based around hitting switches that are blocking barely visible water flow through multicoloured pipes, and you must follow the pipes to find the next switch, despite their aggravating habit of exiting through doors that can't be opened from this side. The real kicker for the Great Bay Temple (and whole game) is that you have a time limitnote which can be tripled by playing the Song of Time backwards, resulting in the "Inverted Song of Time" that slows timeflow considerably for a maximum of 3 hours and 36 minutes. In the other games, you could just keep bashing things in different ways all night long until you got past.
Stone Tower Temple. The two worst parts of it are collecting the stray fairiesnote For one or two of them, you have to do something deep in the temple, then go outside and flip it upside down, then do something else in the same room, then go outside again and turn it right side up just so you can get the fairy. And if you want the Awesome, but Impractical reward, you need all 15 of them, which, unlike the last three temples, doesn't even get you a good reward note In the other temples you get the advanced spin attack, the longer magic meter, and double defense, but the Stone Tower Temple reward is a C-item sword that does little more damage than the Gilded Sword. There's also a room before you get the Light Arrows that involves a Light and Mirrors Puzzle... except that the mirrors actually absorb light when you shine it on them, and you're supposed to use that and your Mirror Shield to reflect the light from your light source to one mirror, then to another mirror, then to a block in your way that disappears when light is shone on it. This wouldn't be so hard if not for the Goddamned Bats that respawn in the room, often messing up your aim at the mirrors. And if you stop shining light on one mirror for even half a second, you have to wait until the mirror has used up all its light before you can recharge it again. There's a Guide Dang It solution that makes it a little bit easier, but it's almost impossible without said solution.
What about the Goron Maze on the Moon? You have to go high speed on extremely narrow ledges, have to bounce off objects at the perfect angle to hop onto another platform, with little room for error. Although this section becomes a joke when you realize that the way to properly do it is by not moving the control stick at all. If you just roll straight, Link will bounce perfectly off the treasure chests for the vast majority of the level.
Oracle of Ages / Oracle of Seasons
Jabu Jabu's Stomach in Oracle of Ages (not to be confused with the dungeon of the same name in OoT) puts all other water dungeons in all other Zelda games to shame. Plus all the other dungeons in those games. Heck, throw in most other dungeons in all other games, too. This place is insane. It's even completely possible to get yourself stuck with no keys, no way to access the boss key, and no way to start the water levels over from the beginning to fix your mistake.
Skull Dungeon from the same game, too. A lot of the jumping is just ridiculous, and there's one room in particular where you have to jump across three moving platforms. If are even a second too soon or too late for the jump, you fall into a lava and you have to jump across each platform all over again.
The Ancient Ruins from Oracle Of Seasons. For one thing, it was huge—the boss battle was on the fifth floor. For another, it prominently featured the Magic Boomerang, which was introduced in the level—which half the time ended up with you accidentally walking into a pit when you hit something and control shifted from the boomerang back to Link. Then there was that mad dash for the Boss Key with the walls closing in... and finally, the boss itself, which required both mad boomerangin' skills and quick timing, all done in a pit of quicksand! With the Quicksand Ring, though, the boss battle becomes much less annoying, as you can move around normally without regard for the quicksand.
The Sword and Shield Dungeon from the same game; between its sliding puzzles on the Ice side, and a few of the jumping puzzles on the Lava side (that take a cue from Skull Dungeon in Ages), can be quite frustrating as well.
Oracle of Ages' version of the Hero's Cave, with its many hair-pullingly difficult puzzles. One particularly aggravating room near the end is full of lava - if you fall, it drops you back on the warp out, "conveniently" resetting the puzzle and forcing you to start it again.
Four Swords Adventures
2-2 of Hero's Trials in the Anniversary Edition. This is true especially if you're playing solo and your DSi's/3DS's L and R buttons do not work. Door two, up until level 3, is a remake of Talus Caves. While Talus Caves is mildly difficult, this gets ridiculous on the second section, where the majority of the level is basically ice. Add on Moblins at the beginning that can snipe you. Add on Ice Wizzrobes. Add on Darknuts. Add on Ball-on-Chain Darknuts. Add on very narrow paths at critical portions. You will cry.
Vaati's Castle section (the last section per level) in each of the three doors definitely count. While they are not "boss fights", the course itself is a boss room. The fans can be quite annoying, and they are less forgiving with narrow paths. Enemy ambushes can be really cruel when the area you're at has rather large swaths of bottomless pits. Worse, you have enemy ambushes that can really drain your rupees. Hero's Trial levels 1-3, 2-3, and 3-3 are the only levels (other than Realm of Memories 1-2) that contain flying tiles, some that respawn. Many people had trouble beating Hero's Trials 2-3 because of an enemy ambush that came in three waves nonstop full of Stalfos and Moblins followed by Fire Wizzrobes and Ball-and-chain Darknut followed by even more Stalfos.
The Minish Cap
The Cloud Tops: like walking in a circle collecting Kinstones and fusing them to random pieces of architecture for no reason other than Padding? And woe to the person who accidentally misses a Kinstone, forcing them to circle around again hoping they don't overlook the same thing twice. The music's nice though, and it leads up to the Palace of Winds, so it's not as bad as it could be.
The Temple of Droplets. Slippy-Slidey Ice World? Check. Marathon Level? Check. The puzzles there caused many players frustration. It's also full of annoying puzzles, especially after you get the dungeon item.
Snowpeak Ruins. The knee-deep snow, the icy floors, the Block Puzzles, the sliding ice things (you know the ones), the Freezzards... the ball and chain does little to abate the hurting. Plus, there's the fact that enemies didn't drop hearts (but you can always ask the nice Yeti for soup. Have fun backtracking to the same room for that, though).
The City in the Sky. Just getting to it is annoying enough, since it requires a huge Fetch Quest just to start another Fetch Quest. It's far too easy to fall to your death, and the level requires precise Clawshotting in order to survive. Plus, it's very easy to get lost in that huge place.
The defending of the caravan. A combination of the Gale Boomerang, needed to put out fires, having next to no range, fast-moving targets, pterosaurs dropping bombs on everything and the fact that Epona handles like she's drunk makes it impossible to beat. It's even harder on the Wii due to the lack of a precise targeting system.
Twilight Princess' version of the Lost Woods has an absurdly confusing layout that the game doesn't provide a map for, not even an overworld map. If that isn't enough to frustrate you, the infinitely respawning Goddamned Bats that go out of their way to hunt you down the whole time you're trying to navigate the place will certainly be. Once you finally get through it, you have to contend with That One Puzzle at the end. And if that's not enough, in order to beat the game, you have to do it twice.
Solmasters. You have to carry a glowing orb through three rooms. A giant hand is chasing you, and if it gets too close, it will snatch the orb back, and unless you want to do the whole damn thing over, you have to grab it out with the clawshot. This requires good aim, and if there are any monsters around, you have to either kill them first or do the targeting really, really quickly. You have to put the orb in certain spots to raise platforms or stairs so that you can get to the other door, which involves leaving it unattended for the hand to grab before you can reach solid ground and clawshot it back up. Enemies can knock it out of your grip, and it likes to roll, so you have to chase it down, and most likely do the whole room over. Oh, and there's two of those orbs, each with their own giant hand. Have fun!
While that's all true, you can also shoot the hands with the bow a couple times to stun them or make them drop the orb. That said, the stun doesn't last long and you'd better make sure you have enough arrows. You can also Clawshot the orb out of the hand's grip if it picks it up.
All the Tear of Light collection quests. Each time you enter the twilight-cursed regions (which have bloom turned up high enough to hurt your eyes), you're stuck in wolf form, which severely limits your tool and travel options. Once there, you have to search all across the region looking for the Shadow Insects that you must kill to obtain each Tear. Except they're invisible, which means you must switch to sense mode, which makes it difficult to see very far. And they're not easy to find, either. You have to do this three times in all; the Lanayru Province can take an hour even at a good pace.
Both of the mandatory wolf mode sections. They take forever, and since you're stuck in wolf mode, you can't really do much. Especially the second section, which prevents you from warping anywhere.
Twilight Princess' version of the Water Temple (which, incidentally, hangs a lampshade on the infamy of the Water Temple mentioned above). If Midna is talked to while in the Lakebed Temple she'll comment on how large the dungeon is and how hard finding all the keys needed to progress will be. Thankfully there's not nearly as many keys in this version. That said, they brought back the annoying key puzzle: You get a key, you open the door, you see nothing but an open space, and you realize you just used the key for the dungeon item on the wrong door. Good luck figuring out the backup Nintendo had set up for you in case you did that. Also, you can glitch your way onto the correct door by jumping from just the right angle.
The Lanayru Mining Facility. The enemies are a pain, the time-shifting puzzles are very tedious, and it's all accompanied with some rather freaky music. Even more frustrating is that this is the temple after the Earth Temple, and the boss of this temple is a joke, making Scaldera seem tough in comparison.
It doesn't help that two of the other enemies there, Beamos and Sentrobes, while being fairly managable normally, become nightmarishly intense on a No-Shield playthrough. And you have to carry the timeshift orbs past them, activating them while your hands are full. Oh, and LMF is actually longer than the next dungeon, and probably the one after that too. It really says something when this game's water dungeon actually inverts this trope and becomes a Breather Level from LMF.
A rare non-dungeon example in the series comes later: the Escort Mission at Eldin Volcano. Basically, you have to escort a robot up the entire volcano, which is now swarming with Bokoblin Archers capable of hitting said robot from afar. (they also have an annoying tendancy of hitting you in the face with a point-blank shot just as you kill them) I hope you've mastered the Bow, because you're going to need it here. And even then, prepared to pull your hair out in frustration as you get through a tough area only to have Scrapper shot down by an off-screen archer when you could have sworn you killed them all. Several times. And it gets worse once you reach the Summit. Think fighting two Lizalfos is hard? Try fighting two while keeping them away from Scrapper, who annoyingly persters you when he's under attack and mocks you when you fail. Even worse, plot-wise, Scrapper not pulling a Leeroy Jenkins would have made things much easier.
Even later, Lanayru Gorge has a case of That One Room. It's filled with Technoblins, Beamos and Sentrobes, all of them either Goddamned Bats or Demonic Spiders, and you have to follow a Timeshift Stone in a moving mining cart to avoid falling in sinksand. Fall in, and you don't take damage, but you'll be returned to the start of the room WITH ALL ENEMIES RESPAWNED! Attempting to put an arrow in a Beamos' eye, missing by millimeters and proceeding to get knocked into the sinksand by its beam... pretty much speaks for itself. What makes this place truly maddening is that its situated after five or so incredibly easy rooms... but there are no checkpoints between them. Having to go back through those easy rooms again every time you die will drive you insane.
The Silent Realms. Similar to the Tear of Light fetching quest in Twilight Princess, the objective is to run through this area and collect 15 tears and then get back to the entrance/exit circle to obtain your next Plot Coupon to get to the next dungeon. Sounds simple enough, except that the area is actually a death trap! Upon leaving the entrance/exit circle, you immediately get noticed by the realm's Guardians that will cause you to fail this test, if they manage to hit you. Obtaining a tear causes the Guardians to fall asleep for 90 seconds, but that doesn't mean much as Watchers are walking around and if they spot you and shine their light on you, the Guardians re-awaken. The music upon being chased by Guardians is terrifying...
And once you have done the Realm for each of the corresponding areas - Faron, Lanayru and Eldin - you think you are done with them forever... you learn that you have one final, extra-hard Realm left to do, which is such a nice kick in the nuts!
The Eldin Silent Realm is probably the worst out of all of them. For one, it's an absolutely gigantic area. The tears are all scattered over the huge level, which is very bad if you've been spotted. And the tears on the large sand slide are the hardest to obtain, since it's a one-way side covered in Waking Water (which instantly alerts the guardians if you step in it) and it's somewhat difficult to get over to the tear by the air current-geysers. Skyloft, too, since even though you've been in that place throughout the game you'll still easily get lost and possibly fall off the place.
A Link Between Worlds
The Ice Ruins. It's a very treacherous Slippy-Slidey Ice World with very narrow pathways and tough enemies throughout the dungeon.