The Legend of Zelda has Gleeok, a hydra monster found in three dungeons. The other bosses are pushovers, but all you can do against Gleeok is stand your ground and hope you have a potion left.
Dark Link takes the cake in Zelda II: The Adventure of Link. He will block nearly every single one of your attacks, and manage to punish every single mistake you make. Not only that, he likes to jump on you and do Collision Damage even though you can't do the same to him. The final nail in the coffin is that he's right after another tough boss, and there is no fairy or healing of any kind between the two, unless you have enough magic (Which is unlikely, seeing how the costly Thunder magic is the only thing that can damage the previous boss). Finally, lose all your lives, and it's back to the beginning of the Great Palace. The fight can be rendered a non-issue by exploiting his AI, but good luck figuring that out as a kid in the 80s.
Mothula holds the title in this game. Erratic movement, randomly-changing conveyor floor, randomly moving blade traps, and a three-beam attack that's hard to avoid if you're trying hard to avoid all the other perils. Worse still, a bug in the original SNES versions made him invulnerable to certain attacks of the level 3 sword and almost all attacks of the level 4 sword (The weak poke is all that works).
Trinexx. You have to use magic attacks to defeat him, which is made a little more merciful by the fact that magic potions are generated in the battle, but still very hard. The worst part, however, is the freaking middle head that bobs out at you fairly often. This will be your downfall in the fight. He gives warning as to when he's going to do it, but even so, it's very difficult to dodge. And if you forgot to pick up the Ice Rod (the location of which which is hinted at by Sahasrahla, but it's found outside of a dungeon and it's in an out-of-the-way area so if you don't pay attention to his hint, you'll miss it), you can't beat his first form, making him unkillable. To add insult to injury, the Ice Rod's projectile moves very slowly, meaning Trinexx'll dodge your shot if given half the chance.
Helmasaur King, the first boss of the Dark World. He takes 25 (or if you use bombs during his first phase, which is more effective but much, much more difficult and slow, 13) hits to defeat. Meanwhile, even if you get as many heart pieces as you can in that point in the game, he can kill you in just 5 hits. If you don't take the time to get the maximum amount of Heart Containers, he can kill you in just three to four hits...assuming you don't take any damage on the path to him, which is filled with tough enemies.
Blaino from The Legend of Zelda: Link's Awakening, for a single charged punch from him will punch you back to the dungeon entrance. He's also almost impossible to hit except when he's preparing that charged punch (which only takes a couple of seconds to charge); if you don't stand in quite the right place while attacking him, he'll hit you and start the battle over. And he has a quicker punch that stuns you, allowing him to land his dungeon-exit punch on you all the more easily. And this guy is the miniboss.
Dark Link is particularly frustrating because he's only a miniboss. This is even worse considering that the actual boss of that level (That One Level through and through) is almost insultingly easy. And if you were hoping to use the Megaton Hammer or Din's Fire on him, they fixed that in Master Quest. You more or less have to beat him in a straight swordfight. A difficult duel could be fun, if there was some technique to it. But your quick-stab is useless (Dark Link jumps on top of your sword, then hits you), your jump attack is useless (Dark Link jumps to the side, then jump-attacks you), and he seems to dodge the spin attack, which leaves madly mashing the standard attack, which Dark link seems to do endlessly with the same speed while locked on, so the blows deflect each other.
Bongo Bongo. Firstly, he's invisible, meaning that you must use the magic-draining Lens of Truth to see him. Secondly, he constantly slams the arena with his palms, which causes you to bounce around, messing up your coordination. You can avoid this by wearing the Hover Boots, but those reduce your traction and practically turn the floor into butter. To defeat him, you must hit both of his hands in enough time, which is especially hard to do when you have three targets to deal with: his hands and his eye. When one hand is stunned, he'll attack you with the other, and you only have a short window of time to act before he grabs you and tosses you into the distance, freeing his other hand (By the way, did we mention that the floor around the arena is made of health-sapping poison?) If you DO stun both of his hands, his weak point, the eye, will open, and you have to react quickly again and hit his eye to incapacitate him before he charges you off the arena. Which can catch many players by surprise way too often. Finally, he has far more health than any other boss in the game, with around SIXTY HP. Hope you brought your optional and hellish-to-get Biggoron Sword!
This game has the hardest boss in the game in Great Bay Temple (Gyorg). The reason is because it has a tendency to swallow the player right after he or she manages to hurt it (for which it's necessary to dive into the water), and it can only be avoided by reacting very quickly and returning to the surface.
Great Bay Temple also has the most difficult miniboss in Wart, a giant moving eyeball that has over 40 bubbles surrounding it to shield it. Those spheres take two hits (one hit with the Gilded Sword) to destroy and after the first, they bounce around making the hookshot useless. And if you ignore the small balls, after enough hits on Wart itself they all fall off and start bouncing around everywhere, making the fight near impossible.
Fighting Goht, which is a combination of Chasing Your Tail and as many hazards as possible, can get annoying. Goht is also annoying in that you need to defeat him more times than the other bosses for the 100% Completion.
Gleeok returns in Oracle of Seasons, as do a bunch of other bosses from the original, but in OoS, he isn't the only boss that can try your patience. Digdogger is especially annoying because you have to fight it by using the Magnetic Gloves to pull a spiked ball into it—and towards you, and yes, it will hurt you if you don't let go in time—and Manhandla, a four-headed Piranha Plant that you have to fight with the Magic Boomerang, the most frustrating item ever devised for this series.
Molgera. You have to get up really close to grab his tongue with the hookshot, but get even an inch closer than you need to and he'll eat you. It's nearly impossible to L-target the tongue after the first time, because mini-Molgeras spawn and get in the way, and it's even harder to target it manually because they'll hit you and interrupt your careful hookshot maneuvering.
Puppet Ganon, since you have to fight him 3 times, with him changing his pattern each time! Especially with the fast third form, an expy of Moldorm from A Link to the Past, where you have to hit it's tail with magic-depleting Light Arrows without the luxury of L-targeting. And especially the third form. Shoot a Light Arrow at the blue ball? Fine. Shoot a Light Arrow at the blue ball on the tail of a fast-moving snake that goes all over the place and never holds still? Better to shoot the guy who designed that phase. Performing an attack at Puppet Ganon's head immobilizes it, but you'll need quick fingers to exploit the narrow gap of opportunity. Those who are patient can jam themselves onto a ledge in the room where the Snake often can't touch Link. The trade-off is the tail becomes more difficult to hit.
The second battle with Phantom Ganon can last forever if the player doesn't figure out the riddle that holds the key to his defeat. Even finding the boss can be a bit tricky, since it requires the player to do something that completely defies previous game logic - yes, you have to jump off the ledge into that gaping, dark abyss, Hero.
The Legend of Zelda: The Minish Cap has the Giant Octorock. The main method of defeating it is to light its tail on fire with courtesy of the light coming from your lamp, but despite the thing's size it's incredibly fast and will often pull a 180 on you before you can completely get behind it. It doesn't help that you spend much of the fight on an icy floor, which means it's nearly impossible to go the right way you want to half the time. And finally you need to stay close by the thing if you want to properly hit it, but this also gives it an easier chance of using its primary attack of sucking you up into its mouth on you. Even if it isn't using the suck attack you'll still automatically be swallowed if you're remotely near it, which can lead to your health being depleted very quickly.
Twilit Bloat, aka the Giant Lightning Bug From Nowhere. You have to fight it on a ring of small platforms, it has a charge attack, and you have to jump on it and bite it to death. If you miss, it gets a free hit. Also, you're essentially helpless in the water, and when it does its rampage attack, the only way to be safe is if you have the agility of a cat on speed. The boss is especially hard if you don't realize you have to use the force field to target and hit all the legs at once.
The second difficult miniboss is the Darkhammer from the Snowpeak Ruins. He wields the Ball and Chain (which is the item you get for defeating him) and is fought in a narrow hallway which makes it very difficult to avoid. He is also only possible to harm from behind, meaning you have to wait for him to attack, clawshot your way across the room so that you are behind him, and then drop and hammer him before he turns around.
The Roktites. A Giant Enemy Crab that waits on the roof of a tunnel and chases you through the mountain while you shoot its eye. After a while its eye only opens if you shoot an Explosive Barrel next to it, and finally it sends jumping minions after you as well. And it runs faster than your train, accompained by the nightmarish music that crescendoes as it gets closer.
Fraaz from the Blizzard temple for various reasons. His attacks are fairly tricky to avoid, and the ice/fire they leave behind then immediately have to be used against him with the boomerang once he switches elements. For extra fun, later on in the fight the boomerang needs to hit him multiple times before he launches the next attack. You have to do this with a measly four, maybe five hearts.
Phytops from the Marine Temple is no joke either. Every time he recovers from a stun, he attacks with two tentacles in a rapid succession that is hard to dodge. In the second half, he also strikes with them during his normal attack pattern in a left-right-both combo that is equally hard to dodge and can easily throw you off the cliff, resulting in another half heart loss.
Skeldritch, the Sand Temple boss, can be a pain, especially due to the sheer longevity of his battle. The first phase consists of catching the boulders he shoots from his spine with the Sand Wand and manoeuvreing them onto catapults before launching them back. Sounds easy enough, but his last few vertebrae are only vulnerable from certain angles, and he continually escalates the speed and intensity of his attacks as the battle progresses. By the time you've reached the last two vertebrae, you'll constantly being floored by his rapid-fire boulder barrage before you can do anything useful, and if you do succeed in catching one, it would be crushed in short order by Skeldritch's next shot.
The final form of Malladus can be a royal pain in the ass if you haven't gotten the upgraded Spin Attack. Trying to defend Zelda and having one fireball hit her and then having her start the whole pattern over again can be rather annoying.
The first couple of fights against Demon Lord Ghirahim are really frustrating, because he can catch your sword strikes with near-perfect accuracy. He's supposed to be a Wakeup Call Boss that shows you that you can't just swing the sword around randomly and hope to win, but even when concentrating and misdirecting him, it's hard to land any hits at all. The fact that he does all this with one hand, lazily catching your sword between two fingers, just makes it more aggravating, as it's clear he's just toying with you.
The second battle against the Imprisoned. The difficulty in this battle is upped considerably from the first fight, as the Imprisoned creates shockwaves with every stomp of its massive feet, making it impossible to come near it and Attack Its Weak Point unless you get really lucky with shield bashes. You're supposed to wait until Groose loads his catapult and stun the Imprisoned with that, but the downside is that this is a Timed Mission; you have to stop the Imprisoned from reaching the temple at the top of the map. In this battle, the boss can grab hold of a ledge and pull itself up, skipping a considerable portion of the map. And the only way to stop it from doing this? That's right, the Groosenator. Which takes him roughly a minute to load after each use. It's not uncommon for a player to stun the Imprisoned with the catapult to land a few hits in, and while Groose is reloading have the boss pull itself higher. And if you save Groose for the times when the Imprisoned pulls itself up? Yeah, good luck approaching the boss with those shockwaves everywhere.
The third fight the Imprisoned is more of the same, up until the spike is driven in. From there on out, it's all the player's aiming skill with the Groosenator, and you can't afford to miss. The first time, it's not so bad, as it's a bomb and those can hit anywhere (but if you miss, consider reloading your save file - the Imprisoned is flying). It's the final shot that's the clincher - you have to aim at the narrow traversable ground on the Imprisoned's head, especially near the spike, and that leaves little room for error. If you aim too low, Link falls, and with the geyser it's not going to be enough time before the rails are crushed and the Imprisoned begins its attack on the Sealed Temple. If you aim too high or too far to the side, it will be almost impossible to make it back in time (there's the central geyser that hops Link back to top, but the time window to use it allows no mistakes at all).
When exploring Skyview Temple for the second time, players will encounter three Stalfos in what was previously the boss room. Later in the game this encounter would be child's play, but this is the first time the game throws so many enemies that require dextrous swordplay at the same time. Considering this is after the third dungeon, when there are still many Heart Containers to be collected, and that Stalfos can knock off multiple hearts with one swing, it's not a pretty fight.
In the last dungeon, you'll have to take on a trio of Stalfos again while a dozen Bokoblins on nearby ledges turn you into a flaming pincushion with their fire arrows. And right before that, you must somehow get past two giant Moblins on a narrow walkway. Both Moblins have unbreakable shields that are as wide as the walkway; hitting the Moblins with your sword is nearly impossible. You could use arrows to kill them, but this only works if you have lots of arrows (you can't leave the room to go get some), and afterward you won't have anything with which to shoot down those archer Bokoblins in the next room. And even if you survive all of this, A Stalmaster (formerly the miniboss of the Ancient Cistern) will await you at the end.
Scervo, the ridiculously frustrating miniboss of the Sandship. No Ring Out Boss should ever have that much knockback. The fight takes place in a narrow, fenced-in "plank", so there's only one direction you can drive him out. And he's fast. He will hit you. A lot. It takes a second or two for Link to recover from the force and run back in, giving Scervo the chance to close the distance. And it's not enough when you finally manage to get him to the edge; you have to do it three times.
The final fight with Demise is exceptionally annoying. First, you have to hit him endless times avoiding his quick attacks, and if you get too far from him he just runs towards you, slashing you with his sword. Once you finally manage to make him fall to the ground, he gets up again, summons a STORM and charges his sword with lightning. Now you'll have to avoid both his skyward strikes and his regular attacks, exposing yourself every time you charge your own skyward strike, which is the only effective way you can stun him. Once you have managed to make him fall once again, you'll have to repeat the same process at least once more, and finally deliver the final blow. Oh, and make sure you're quick enough, because he'll get up right at the last moment. Have fun.
Zaganaga, the boss of the Desert Palace, is a tremendous pain. The arena is one big quicksand trap with small pillars that you can stand on dotted throughout it; the boss pops out of these pillars at random, and you have to use the Sand Rod to raise temporary platforms so you can get close enough to hurt him. Thing is, the temporary nature of said platforms means you may or may not have enough time to run all the way up to Zaganaga and slash him, and the whole time he spits out dozens of Peahats that fly into you and knock you into the quicksand. Making matters worse are the long-range beam attack he gains after he Turns Red, and the fact that he seems to have a lot more health than other bosses. At least the Sand Rod can be upgraded to the Nice Sand Rod so that the platforms it creates don't disappear, but it's not going to help too much with the Peahats and beam attack if you're not fast enough.
Knucklemaster replaces Mothula as the boss of Skull Woods, and it's no less aggravating. Its punch attack is very difficult to dodge, and requires quickly merging into a wall to avoid so it can crash into a wall and be vulnerable. Damage it more, and it gains a slamming attack that's also difficult to dodge, and destroys the ground you fight on, making it even harder to avoid its attacks. When it Turns Red, things go downhill fast. Its slams are faster, most of the walking space will be destroyed at this point, and every time it's left vulnerable, you'll get maybe three hits in before it starts attacking again. It can be skipped, but unless you've got a specific item to dodge its attacks, good luck.
Dharkstare, the boss of the Ice Ruins, is also a pain. First off, the arena is an icy surface, which means you'll slip all over the place, and is surrounded by a Bottomless Pit, and there's also a pit in the middle as well. Dharkstare never holds still, making it extremely difficult to melt its ice shield off with the Fire Rod, and it attacks by sending three energy balls out around your position in a triangular shape which after a few seconds freezes the area inside it. Unless you're already moving when it sends the triangle out, good luck not getting frozen. Oh, and when it Turns Red, it starts sending out a second triangle.