Chrono Cross gives us the Dead Sea. It pulls off the hat trick of 1) a confusing area peppered with tough battles (including the Tragediennes - and you'll want to fight them to get overpowered elements), 2) That One Boss (the infamous Miguel), and 3) marking the point at which the game's plot begins to topple in on itself.
Terra Tower. At this point, Ending Fatigue is in full effect. Terra Tower is a long uphill climb to reach the Dragon God. It's swarming with TerraTerrors and has several Goddamned Minibosses, as well as a sizeable Info Dump halfway up. Just to add to that, in a game known for Scenery Porn and awesome music, the backgrounds are dull and a large portion of the tower has no music, just generic ambient sounds like running water, which turns Terra Tower into an interminable slog. What were they thinking?
Kingdom Hearts has the Atlantica level. In fact, it's easily the most reviled level in the game, though Monstro (which comes directly before it) is heavily competing for the title.
The sequel still has Atlantica, but replaces the swimming with an even more annoying musical Rhythm Game. Thankfully, it's optional.
Chain of Memories's Atlantica doesn't differ from the rest of the game much, although the Shadow Heartless are replaced with Sea Neons. Then again, Hundred Acre Wood replaced it due to how slowly Pooh walks and how he rarely follows you very reliably (like when you have to climb up on the cart or do the "bouncing game"). Thankfully, the Updated Re-release on the PS2 fixed this.
In Kingdom Hearts II, Port Royal also gets this treatment by some fans, as it is simply a Theme Park Version of the movie with Sora, Donald, and Goofy barely involved in the movie's story, plus frustrating combat against cursed undead pirates.
Space Paranoids isn't all that hard, but the Light Cycle sequence is truly hellish, mainly due to how the damn thing controls. And if you aren't able to read your opponents' moves before they happen, then you're just screwed.
358/2 has the forced Stealth-Based Mission. It wouldn't be so bad if Axel didn't have a tendency to just stand around and let himself get caught. Or that Kingdom Hearts always had a slightly wonky camera system that sometimes is more of a hindrance then help.
Keyblade Graveyard's Twister Trench in Birth By Sleep. There aren't any enemies here, just massive, multi-colored tornadoes, that chase you all over the map. If you're caught by one, you're thrown into an alternate dimension with several waves of giant Unversed. Although after you beat one it goes away, it's so hard to dodge the next that it's really simpler to just fight them all.
The Cavern of Remembrance in Kingdom Hearts 2Final Mix +. It's a chore in itself to make it past the platforming puzzles of the Mineshafts (and it's downright impossible if you haven't leveled the correct Drive Forms enough) and the forced fights against Demonic Spiders in Heartless' clothing, but after you make it past all that, you still have to defeat waves of Nobodies that can kill you very easily if you're not careful. Your reward for surviving through all that is gaining access to the Data Organization XIII battles, each of which make the aforementioned torture seem easy in comparison.
Kingdom Hearts coded and re:coded get in on the frustration with Hollow Bastion. As soon as you defeat Jafar in Agrabah, Malificent breaks your keyblade, barring you from using any commands or even breaking blox, and you're put through a gauntlet of maddening timed platforming before you spend the rest of the world with Goofy and Donald. This generally involves giving them a command then waiting around for their dismal AI to pull it off, and though they're generally effective in combat, Sora cannot attack in any way and can only use potions. At the end of this, your keyblade is restored, and then without time to even switch commands, you have to fight Pete, Pete with D-Thundaga, Riku, Riku again, and a far more dangerous Riku. Even then, you're thrown into Riku's datascape where your stats are horribly weakened until you restore them. You cannot leave or revisit past worlds during any of this.
Steamwood in Brave Fencer Musashi. Imagine, if you will, having a slowly rising bar. When it gets to the "OK" zone, you press X to fill another bar until it gets to the top. Now imagine the first bar going inhumanely fast, requiring you to either use skillful Button Mashing or to have completely superhuman reflexes, and each hit filling up only a fraction of the second bar. Furthermore, you generally have 35 seconds to get to the next valve (60 if the game's feeling generous) and complete this task before you start over from Valve 1. Oh, and if you miss the OK zone, the second bar goes DOWN.
And that's just the first time. The second time, several of the wheels aren't even attached to their respective valves, so you have to go find them. While dodging steam leaks. With your only means of travelling up levels an irritatingly-slow elevator. And jumps that can easily cause you to plummet back down to the bottom.
The Road to Rhone in Dragon Quest II definitely qualifies. It's long, inhabited by the strongest enemies in the game by this point which attack frequently, and features rooms full of hidden trapdoors that send you back to a much earlier point in the dungeon if you step on them, made all the more infuriating because of the final piece to the MacGuffin hidden in a completely non-distinct tile. Even if you find the dang thing you still have to walk all the way out just to complete said MacGuffin (on the other side of the world no less). Part of the reason this game has a well-deserved reputation as Nintendo Hard.
There isn't even a saving grace once you get to Rhone itself. Even stronger enemies, many of whom will self-destruct and take 1/3rd of your party with it, a blurry landscape thanks to all the snow, and the only save-point is in a shrine nestled in the middle of a lake far from the cavern's exit.
The Dharma Temple in Dragon Quest VII fits this trope to a T, as well. Dharma Temple being the place you typically obtain new classes and skills in Dragon Quest, instead you're thrown into an extremely difficult dungeon that you cannot exit while having your skills sealed away. Good luck if you didn't think to buy any Medicinal Herbs beforehand!
Riki's Mosperiburg dungeon in SaGa Frontier. A room with a narrow, invisible path you must use to walk over spikes, with a random battle occurring each time you touch a spike, and the path is diagonal to increase the chances of you walking off the path; another room where you must fight 30 durable Magma Slimes that hit your LP, which is like your HP except it's game over if Riki loses all of his; and a non-standard Boss Battle where you must perform a variety of combos that need to use three to five characters each. Yay? This can be bypassed if you use: DSC (Self Linking Combo)
Xenogears, Tower of Babel. The way the game works, if you get into a battle in mid-jump (and you will), you drop like a rock afterwards. Add lots of platforming, moving platforms that double as monsters, and you've got a recipe for frustration.
Not to mention the inability to use the analog stick...
And let's not forget a few awkward jumps on the lower levels that it takes an hour and a half just to get right the first time
If you only move after starting a jump, you'll never initiate a random battle. (So in theory, you could traverse entire areas with no encounters.) However, even if someone tells you this before you waste a lot of time falling out of the sky it's still a very tedious way of getting through jumping puzzles.
One last bit of frustration for that level comes from Gameplay and Story Segregation. The Tower of Babel is a vertical platforming dungeon, but it is also a gear dungeon. It is shown several times before AND afterwards that your gears can fly.
Secret of Evermore has a maze where you control the Dog and have to escape by running around air ducts in the castle. Turns out all the ducts lead you around in one giant circle - the duct that leads out is hidden behind a bookcase out of your view and thus you'd never know it was there.
How about the path under the waterfall? You're in the dark, all the paths look the same, there are no save points or shops here to restore yourself, and there's a constant supply of respawning enemies.
And then there's the Dark Forest, an endless maze of trees with dead-ends and lots of enemies, you will get very lost very fast. The game is merciful by giving you a subtle hint - the trees in the foreground sometimes have demons in them, and if you follow the paths with the demons you'll find the exit. Of course, the game never tells you this. And to add to the insanity, when you get to the bridge and beat the boss, you find out it isn't over - the forest is split into two sections, you've still got Part 2 to go, and Part 2 also has a boss.
While probably not as infuriating as some of the above examples, the Junkyard area in Legend of Mana definitely qualifies That One Level. Paths change with no warning, depending on if you talk to certain NPCs or not. Certain paths become inaccessible if you happen to change your mind and go another direction. Towards the end of the level is an NPC that will teleport you all the way back to the beginning, from where you'll have to struggle all over again to get back to where you were. Even with a guide, it's difficult to navigate as you have to talk to or ignore certain NPCs whose helpful advice consist of lamenting to you in vague terms. Pair this with mandatory encounters on certain paths, and you have yourself a scrappy level indeed.
The 13-floor Bonus Dungeon Pork City in The World Ends with You. On every floor, you're confined to using one brand of pin and unbranded pins, which will especially suck if there's a brand whose pins you don't give a crap about. Worse yet, the Noise in this level consist almost entirely of Goddamned Frogs; namely, red Brassbanfrogs that absorb long range attacks, and yellow Tradishfrogs that dish out plenty of damage. And of course, on the roof after clearing the 13th floor, you face That One Boss Panthera Cantus, who can kill you in 2-3 hits even if you are at level 100.
This "difficulty" is heavily mitigated the moment that you realize that Angel and Reaper class pins are unbranded. Which, simply put, means that you can equip them on any floor you want. Although obtaining them typically requires bumping the difficulty up to hard to beat various noise, it helps greatly.
The infamous Battle of South Moundtop scenario from SaGa Frontier II. The condition for winning are either defeat Fake Gustave or survive for 8 turns. Since Fake Gustave and his steel soldiers are virtually invincible, you're better off trying to hold him for 8 turns, which is also very hard. If his troops kill your leader or they invade your base it's all over, and Fake Gustave and the steel soldiers can get really quickly into your base. He will usually only move on the 4th or 5th turn, but if you dispatch of his infantry very fast he will start moving earlier, making the scenario Unwinnable.
Worse than Manaan is the Star Forge. Nigh unlimited enemies, no way to leave, and a luck based battle system that makes you save before every encounter in case your rolls mess up and kill you. KotOR was fairly forgiving up until that point.
The most unpopular example by far is the Taris swoop race, a mandatoryUnexpected Gameplay Change into an exceptionally cheezy racing minigame.
More annoying than the swoop race is the mandatory shoot-them-up mini-game that pops up as soon as the Ebon Hawk takes off Taris. The worst part about it is that if you lose, you'll have to rewatch minutes of unskippable cutscenes. And that's assuming you saved just before boarding the ship, and not earlier. And that your game doesn't crash right after you finally win it, as several players have reported.
Knights of the Old Republic 2:
The Peragus level and the main Trayus academy. Running speed in space is no longer a problem (probably due to the Manaan complaints from the first game), and neither is difficulty, but they are just so boring, with little payoff compared to the amount of time spent running around.
Malachor V. If you don't kill all Storm Beasts while you play as the Exile, your chances of surviving there as Bao-Dur's remote are close to zero.
Nar Shaddaa, near the end of its questline. Attractions included: no Player Character, fighting your way through trained killers as new, non-Jedi character (Mira), facing bounty hunters with non-Jedi characters most players wouldn't otherwise pick (Mira, Atton, T3- M4) and storming Exchange's boss heavily defended yacht with only two squadmates, who WILL get stomped, even if you pick stronger ones (like Kreia).
The Highcliff castle. It's full of ghouls which have a stunning attack, and they actively use it to render your party immobile. Then they proceed to Zerg Rush you and wipe you out with regular melee attacks, reapplying the stunning effect over and over and not letting you break free. This is the case of a screaming need for a mage in the party - however, by that point of game, you haven't recruited one yet (except for Elanee, but she has only one offensive spell), and if you play as a mage, your own level is too low to have spells which would be effective in this situation.
The final level qualifies for this. It's the only level in the game with infinitely respawning, sometimes annoyingly difficult enemies, its design is a confusing maze with teleportation doors, thereby preventing you from making a beeline for the exit without fighting hordes of powerful undead, and if you attempt to rest, enemies will interrupt you, thereby preventing you from recovering health and spells. After this, there is an obnoxious miniboss fight against three Shadow Reavers, possibly qualifying for That One Boss.
The Underground City/Maze level. With the party AI's very poor path-finding ability, it was a complete bitch to navigate the very narrow maze, while avoiding tough undead warriors that are immune to slash attacks and has a fair amount of magic resistance. You also cannot rest anywhere without getting ambushed by said enemies. Which is bad, because a monstrously hard Boss Fight is at the end of this scrappy maze.
Also, the Firewine ruins. It is basically the Underground City, except this one also has endlessly respawning Kobold Commandoes in it and you start in the middle, with only one route out of three being the way out.
Châteu Irenicus in the sequel. It's not a really difficult dungeon, nor is it really that badly designed. But if you like making new characters and replaying the game, ye gods will you grow tired of it.
Therum, which is most likely the first story planet the player will go to upon leaving the Citadel. It starts out with a long drive in the Mako, consisting mostly of plowing through geth outposts. It's not too difficult, but if you're not used to the Mako's handling, it's way too easy to plunge into the lava or get slaughtered by Armatures. After a while, you leave the Mako and fight through several waves of geth, eventually coming up against a squad of geth infantry and an Armature, which can easily one-shot a low-level Shepard. Then, you enter the mines to find Liara, and have to fight a Wake Up Call Boss immediately afterwards. At higher levels, it's not too bad, but most players will want to fill out their party as soon as possible.
Oh, and just for fun, both the Armature fight and the boss fight against the Krogan Battlemaster? Both preceded by unskippable cutscenes before the fight but after the autosave (since you can't save in combat, that means you start from before the cutscene). The run-up to the Battlemaster fight must be going for some kind of record, as it is preceded (between autosave and fight) by an unskippable dialogue, an elevator loading screen, and then another unskippable dialogue before going straight into the fight.
There's also the dreaded moon base. You initially hear about that mission (in which a VI has "gone rogue" and is defending a lunar base with approximately ten million rocket drones) fairly early on in the game (it's triggered by hitting level 20, which doesn't take a long time). Three bases full of drones, half of which are equipped with rockets that can kill you nearly instantly. Good luck if you actually try to go and do it immediately after getting it.
Planet Nodacrux, the location of the follow-up mission to Feros. Known among fans of the game as "Oh please God no, not that planet!". Its an example not because the mission is overly difficult (its a simple smash-and-shoot, actually), but because Nodacrux is covered in what comedian Buddy Hackett used to call "big, gigantic, mean-looking, evil Nazi mountains" that you have to somehow climb over in the Mako. On average, it takes a person ten to fifteen minutes of mountain climbing just to get to where you can get out of the Mako and spend a minute and a half shooting Thorian creepers.
The "Pinnacle Station" DLC has one in the form of the Subterranian survival map, in which you must survive for over 2 minutes and 20 seconds against an army of rocket launcher equipped geth, including Geth Primes which you only encounter a couple of times in the main game and always appear when you can use the environment to kill them. This time you have to kill them the old fashioned way.
Ahern's survival mission is even worse. You have to grab a data cache, then hold out against infinite waves of fully armored turian soldiers for five minutes. There's only two plausible defensive positions on the map? And the soldiers use rocket launchers and tech sabotage too? The only help is that you can hack two automated but slow-firing turrets to help you.
Horizon. It's the first mission against the Collectors, and you're up against everything they have. It starts off with simple fights against Drones, then throws in Assassins, Husks, Harbinger-drones, Scions, and finally a boss fight against a Praetorian. Later on, this is normal fare, but it's difficult here because it's quite early in the game; none of your (non-DLC) party members have their bonus powers unlocked, there's minimal weapon choice, and you're at a fairly low level to boot.
The disabled Collector ship. When you first get attacked by the Collectors, they trap you on small flying platforms and fly in reinforcements, consisting of all three Collector types, as well as two Scions. This doesn't seem too bad, until Harbinger ASSUMES DIRECT CONTROL of one of the Collectors. Harbinger excels at knocking you out of cover, especially low cover, which is all you get on the platforms. In addition, the Praetorian fight later on in the mission is a pain, especially considering you have to deal with Husks and Collectors while you fight. What makes this level the worst is the very first minutes: You've got incoming platforms filled with Collectors while one platform sits outside the field of battle with a Scion on it, constantly moving back and forth from two positions which are GUARANTEED to flank you wherever you are. On Insanity, this means getting torn to shreds whenever you pop out of cover to take out said Scion, or it means getting torn to shreds after Harbinger knocks you out of cover while you're having to recover your shields from a direct Shockwave blast from a Scion, which prolongs your regeneration by precious seconds. Hopefully, you should have been getting whatever offensive and defensive upgrades are available by that point...
Archangel's recruitment mission is another tough one. Once you reach Archangel, you have to defend him from a large group of advancing mercs and mechs, including a boss. That's the easy part. Now you have to go down into the basement to shut emergency shutters to prevent enemies from breaking in. This section is full of vorcha, varren, and krogan who can eat through your shields and health quite quickly (and most of them have regenerating health). Next you have to fight another boss, who makes a beeline straight for Archangel while his mooks pin you down. Finally, you have to defend Archangel against a swarm of mercs while a gunship takes potshots at you. Oh yeah, and you've got a "time limit". If Archangel's health is depleted, you lose. This mission is especially nasty on Insanity, rivaling Horizon. The shutters deserve elaboration. You press a button and a ten-second timer starts counting down. If anything crosses the shutter's path, the shutter declares it unsafe and aborts the closing process. The first shutter is easy; if you sprint to it and hit the button, by the time vorcha start pouring through into the tunnel beyond, the shutter will be closed. The shutter to the left takes you down a very narrow corridor with pipes blocking the path, and vorcha hunkered down behind the pipes. It gets especially nasty if there's a Pyro behind one of the pipes and you don't realize it, because he will stunlock you to death the moment you jump over the pipes (and if you do realize it, a corner detection glitch means that you can't kill it with powers without jumping over the pipe). On the right hallway, you come to a very open room, teeming with vorcha and varren. They endlessly respawn through the shutter, and the room is so big that by the time you've killed the ones up close, the far end has been fortified with vorcha and krogan. And when you do get to the shutter, you better hope they don't unleash varren, because they run fast enough to interrupt the shutter and restart the countdown.
The Derelict Reaper. The last part where you need to destroy the core and fight wave after wave of Husks is near impossible on Hard/Insanity. The core only being available to attack for short periods which you can easily miss because you're too busy staying alive doesn't help.
And in "Lair of the Shadow Broker", the mandatory car chase. Good luck trying to steer with low mouse sensitivity. You may also have to disable motion blur because otherwise you'll end up trying to drive an indistinct, well, blur through a completely black screen.
Tali's recruitment mission is very difficult as well, more specifically the end fight against waves of infinitely respawning geth and a colossus which keep you pinned down with suppressive fire at essentially all times, as well as the fact that any area touched by the sun drains your shields. Did I mention that the only way to get the Geth Pulse Rifle is to play it on Hardcore or Insanity?
The final level. A nasty Difficulty Spike and a jarring shift in tone combine to make London a thoroughly unpleasant level. For starters, it throws seemingly endless waves of every variety of husk at you, all while you scrabble around to find a decent chest-high wall to stand behind. Then, in lieu of a final boss, you have to deal with anywhere from four to nine Boss in Mook Clothing types, all of which can kill you in two hits—whilst dodging a Reaper laser, which is a One-Hit Kill. While none of these elements themselves are that difficult (or, really, together either), there is simply no margin for error: either you fight perfectly or you game-over. It's even more painful when you compare it to the Suicide Mission in Mass Effect 2.
Grissom Academy... at least in London it's the endgame, so you have all your party members, some high-end equipment, and probably several skills maxed. The Academy is very early, so none of those options are available to you—and you can't shelve it for later like other non-priority missions, because the game automatically fails the quest if you don't do it past a certain point. The mission itself is hell, with multiple Atlas Mechs backed by Centurions, Guardians, and—worst of all—Engineers. You know, those guys who drop party-killing turrets and heal Atlases. The fight in the atrium—where Centurions cover everything with smoke, Engineers lay down turrets near shield pylons, and Guardians constantly advance on you, all of which get covering fire from an Atlas—is easily one of the hardest firefights in the game. And at the end of the level, where they have the decency to give YOU an Atlas, you still have to Hold the Line against multiple waves of troops and other Atlases, more or less guaranteeing that your own mech is going down before the fight is over. Even more so than London, players contend that this level is Mass Effect 3's most difficult.
The friggin' Geth Dreadnought. First part of the mission? Several landmines are planted all over the ground that you can easily step on that will drain your shields and health, which leaves you wide open to an attack if a Geth attacks you. Then things get even better for the second half. Now you're in a section where a shockwave reguarly blasts out every 5-10 seconds and drains your shields away and the only way to not get hurt is to take cover, only sometimes even if you are you'll still get hurt. Couple that with the fact that the Geth in this section completely overwhelm you and you will definitely have to replay this nightmare multiple times.
The final battle of the Tuchanka arc. Remember the One-Hit Kill Reaper beam mentioned above? Not only do you have to constantly dodge that, you also have to avoid being stomped on by said Reaper, while fighting about six Brutes. To make things worse, the battle takes place in a small enclosed area with no cover, meaning that you'll often avoid one Brute only to stumble right into the next or get hit by the Reaper's attack. It only gets worse if you're playing an Engineer, an Adept or an Infiltrator, because those class fare badly in melee, which is impossible to avoid here.
The portion during the Circle of Magi quest, where A Sloth Demon sends you to the Fade, WHICH YOU CAN'T STOP AT ALL, and you have to fight through dull environments, barely any dialogue, tons of fighting with very strong enemies and the Final Boss himself goes through about 5 different forms before he dies.
Orzammar. Long, dull, repetitive, predictable, and nary a third option to be found anywhere, least of all in places where the first and second options are both equally stupid. And nearly as long as The Brecillian Forest, Redcliffe, and the Circle Tower COMBINED.
The outside of Fort Drakon, where Dragon Thralls attack alongside many ranged Darkspawn. If you hold back, the Emissaries will kill you with their spells, and if you charge, another Dragon Thrall appears. The General battle in the Alienage is also quite difficult, since infinite Darkspawn pour in as you're fighting.
Tales Series (Namco)
The Morlia Gallery in Tales of Phantasia from the floor B11 and down is undoubtedly the hardest of all game. Reasons you might ask, there are some. You can't use Light Bottles which decrease the encounter rate, which happens after every damn 10~15 steps. Some puzzles are very annoying to deal with, mazes in dark rooms with faint blinks and then there's the poison fog which will slowly drain your HP getting you off guard and making it low enough for enemies kill ALL your party member with a single skill. What's better? You still have more ten levels and it's all downward from there, bonus with the music getting more and more twisted and creepier every floor you manage to go down.
Try to fight the enemy called Urchin. YOU. WILL. REGRET. IT.
Speaking of enemies, there are combos like Manticor and Beast Man which will cast two spells, giving you almost no time to interrupt them, that will most likely kill your entire party even with capped HP or tear a good chunk of it. Get near it and Manticor will pummel you to death and Beast Man will Hell Gem until you're grounded, also not letting Mint Heal you.
The Beastman/Tuskboar combo is worse. You CANNOT run away, period, because the meter countdown resets every time you get hit, and the Tuskboars will be hitting you constantly. What's even more fun is that Beast Man's "Summon Lich" spell can't be blocked, and will do massive damage to your characters, even if their defense is maxed out.
Wild Wolf damn it.
Mimm is almost as difficult as Beast Man. She casts powerful magic, but her worse attack is to throw up a shield that takes a huge chunk out of your character's HP if they touch it. And she flies around, so you can't just keep your characters away from her.
The Temple of Fenrir from the same game. A rather simple ice-based dungeon that isn't slippy-slidey... but it's huge and is home to the Ekim, a monster that is rather simple to beat when there's one, but if there's 2, hope to run away before the first God Breath (Judgment in the GBA version), because beating 2 Ekim is impossible- the first will charge you, preventing you from interrupting the second's God Breath spell, which will hit you for about 2500 damage and leave you stunned long enough for the first one to have cast the spell- hitting you again, and chaining you until you die.
And The Tower of Flames. Tower's a pretty standard Lethal Lava Land in RPG terms, fire enemies, lava flowing around, but here's the catch... Convection Schmonvection, right? WRONG. DEAD. WRONG. If you dare set foot in a room that so much as has a crack in the floor where the lava flows underneath, any character who isn't equipped with an item that is only mentioned through a really vague hint, and can only be obtained by transforming another item thatRandomly Dropsin the Tower of Flames off of theGoddamn Bats of the area, takes massive damage very, very, quickly. Then deeper in the dungeon, should you decide to heal through the damage (it can be done, but your resources will be exhausted quickly) there's a room with lava... everywhere. Entering this room without the item can't be done (and if you make it that far to see the "The room ahead is far too hot to proceed" message, you're probably going to die from being out of Gels and TP), and if only some characters have it, the ones that don't are killed instantly.
The Meltokio Sewer is a complete pain (dear god the sliding block puzzles), coupled with bad background music.
The Temple of Darkness is easy, except for the fact that the AI of the Shadow Blobs that you have to lead to the bottom is absurdly stupid, and the path to the seal is full of twists and turns.
The Book of Forbidden Anamnesis is entirely luck-based. To be fair, it IS a Bonus Level Of Hell.
Worse than that in Dawn of the New World: Gladsheim. 8 by 8 Square with rooms that randomly interconnect, tons of (thankfully weak) enemies, and you pretty much have to fully explore each of the 10 Floors in order to proceed in the dungeon. Oh, and what you went in there for, Marta's Kismet, yeah, the Bonus Boss at the end only has a 5% chance of dropping it.
The Temple of Lightning. Only has the bolts of lightning coming down from the sky in the sequel (though both have plenty of electric hazards), but both games have those goddamn dark twisting chambers.
That, and the backtracking, the visual dullness, backtracking, the random encounters that can easily kill you if you're not paying enough attention, and the backtracking make the Temple of Lightning an egregious pain in the ass. Even the Game FAQS guide starts to make fun of all the backtracking you have to do in there.
In Tales of the Abyss, the world map has a lower frame rate than towns and dungeons, which means you move slower, and if you have to rotate the camera, it swings around extremely slowly, however, enemies don't seem to move around any slower. Also, after battles, the world map takes significantly longer to load up than dungeons do. So, let's put not one, but two dungeons technically as part of the world map, and stick extremely annoying factors for both!
Inista Marsh - you move even slower than you usually would because, well, it's a marsh, the ground is unstable. When you're going through it, you have a chance of running into the Behemoth, a monster that can kill you very quickly and easily, and if you defeat it it will not drop anything, not even experience, and it will still be able to attack you again. And Tear's title that prevents encounters has no effect on it at all.
But Holy Bottles DO. Down one and the Behemoth (and every other monster) will run away from you for as long as the effect lasts.
Meggiora Highlands - You need to go here twice. The first time, it's a timed mission. Technically you don't have to complete the mission on time, as the game will still progress in the same way if you don't, but a friendly and harmless NPC dies. The second time, it's impossibly huge, and if you want to make the boss at the end a bit easier and get all the dungeon's loot, you have to solve four very irritating block-style puzzles.
Tales of Legendia has the Forest of No Return and Mirage Palace. You'll be glad Moses allows you to skip the Forest of No Return and that Will can make you skip the puzzle in Mirage Palace. However...they're repeated. The Forest of No Return must be forded through once more. Thankfully, Mirage Palace can actually be gone through by mistake.
The sewers from Vampire: The Masquerade – Bloodlines. A long, visually boring slog through an unintuitive maze, in which the basic enemies were somewhere between Goddamn Bats and Demonic Spiders, and which had degraded bosses that appeared as boss fights earlier in the same level, and no sources of health except for rats, which Ventrue can't feed on. There is an item which allows one to replenish health by defeating enemies, which makes this bit much much easier, but the quest chain for getting that item involves going to the museum, which is a Scrappy Level in its own right. And even this item only makes the sewers bearable; it doesn't do a thing to make them fun, or to mitigate the fact that (apart from Chinatown) the sewers mark the point at which the game shifts away from the story- and character-driven gameplay that made it a Cult Classic, and toward one endless combat section after another. And it never shifts back.
One of the game's developers later said that if there was one thing he could change about the game, it would be cutting off half of the sewers.
The Ocean View Hotel qualifies on the second and later playthroughs. The first time around, it's creepy and atmospheric. Subsequent runs through the hotel reveal it to be an overly long linear crawl through a haunted house comprised entirely of tired horror movie cliches. This one's especially interesting because, in spite of the game's strong, long-lived cult following, the only major awards it ever won was for "best level" for the Ocean View Hotel. And while one of the things that makes the game special is its abrupt genre shifts (in this case into survival horror), anyone who's played the Ocean View Hotel more than once thinks of it as "that place where I can't die and where I have to do a lot of tedious up and down maneuvers."
Adding insult to the Disappointing Last Level's injury, the Final Boss is literally impossible if one does not have a gun, and very nearly so if one does not have the skills to use it (unless one hits it with the conveniently placed searchlights, thereby paralyzing it and bringing it within easy melee reach).
Wizardry: Proving Grounds of The Mad Overlord. Level 3. Gah! I hate the 3rd level. Pits everywhere—and you have to walk into one before you can map it, which is why most players skip it using the elevator or they find a clear path to the stairs to level 4 and never explore the rest of the level. Other levels have pits too.. but the 3rd level is the worst. And then I think it's about level 7 when the ^$$?@@! vampires show up. They hit you once and you get drained 3 levels or so—which usually by that time represents several days worth of play time. All you can do is send your Samurai or Ninja after them, hope they get initiative and a decapitation, otherwise prepare for the hurt.
Fortunately, those levels are entirely optional — the only floors you have to visit are 1, 2, 4, a tiny part (4 spaces on a 20x20 map) of 9, and 10.
In fact, you don't even have to do that, at least in the original (Apple II) version. Casting MALOR in combat has a chance of randomly teleporting you to level 9, a short walk away from Werdna's lair. (Of course, if you're not cheating, you'll probably want to visit the other levels to gain experience and items first.)
The Gehennom levels of NetHack are often disparaged by players, not because they are hard, but for the exact opposite reason: after spending the first 30-odd levels scrapping along, fighting for your life every step of the way, you now have to plod through endless twisty corridors, mechanically chopping down enemies, with only an occasional demon-lord to break the monotony. This wouldn't be so bad except there are about 20 levels of it. Finally you reach the Wizard of Yendor and the challenge-level zooms back up again. There are magical ways to speed up the process, but still.
And making it even worse, once you get the item you went down there for, you have to walk all the way back out because the item prevents you from being able to teleport between dungeon levels.
This is one of things the NetHack variant Slash'EM attempts to fix, by shortening Gehennom while adding more special (ie dangerous) levels.
Ancient Domains of Mystery's "Tower of Eternal Flames" is four levels tall. Every step on every level causes damage and has a decent chance of destroying some of your equipment or inventory. Both of the effects can be somewhat mitigated, the damage by fire resistance and the destruction by blessed rings of ice and fireproof blankets, but drakelings take damage even with fire immunity and the two items are not perfectly effective. On the top level, you have to tunnel to the Fire Temple, which is disconnected from the rest of the level. This requires certain items, which of course may have been destroyed earlier in the Tower. Then, in the Temple itself, there is a very large number of dangerous enemies, including one of the nastiest bosses in the game.
The Isle of Crypts in Wizardry VII: Crusaders of the Dark Savant]. I dare you to try making it through this trap-infested hell that's crawling with powerful enemies and some truly evil puzzles without a strategy guide. If you've collected the various optional map pieces along the way, you'll at least have some hints on how to solve the puzzles, and holding on to a couple of items you may or may not have picked up near the beginning of the game with no obvious use then will tone down the traps a bit, but if you were lax in exploring the City of Sky, didn't get one particular Plot Coupon out of the dozen or so out there, or haven't been paying close attention to the game's mythology, your progress will come to a dead halt.
And then there's the Tomb of the Astral Dominae itself, at the bottom of the Isle, but mainly due to the enemies you'll face. If you know what to expect and have built your party accordingly, the battle droids are tough but managable, even the Cosmo-Bot. If not... get ready for even more hell as plasma cannons scythe through your party, especially the back rankers, and your spells make the enemy giggle, coincidentally turning the Cosmo-Bot into That One Boss. And then the Big Bad and his elite guard show up... oh, and did I mention the puzzle madness doesn't stop down here?
The entirety of Eye of the Beholder fits this trope, both because it's Nintendo Hard, and because the game saves automatically when you rest (which can be problematic if the character you thought was unconscious is actually dead.)
Are you talking about the PC, SNES, or GBA version? I've only played the PC one but it wasn't that hard, and it didn't autosave, ever.
The PC version didn't autosave and was actually quite easy. Except for the spider level which is actually.. that one level.
Avernum 4's Eastern Gallery manages this entirely through Demonic Spiders, giant insects known as chitrachs. They're fairly hard to hit, they have high HP and damage resistances, and every time you perform a melee attack on them they have a chance of blocking and damaging you. Oh, and there are 227 of them out for your tender flesh. Enjoy!
In Arcanum: Of Steamworks And Magic Obscura, the Black Mountain Clan is terribly annoying and where you will probably encounter your first Difficulty Spike. Unlike every other part of the main quest, you can not talk your way through or around it and it is a required dungeon crawl. The halls are littered with traps, being the only area in the game to include them so extensively. Also, most, if not all of the enemies in the mountains are made of rock or lava, and damage your weapons if you hit them and your armor if they hit you, making that part even worse for melee fighters. Most annoying, however, is that the lead you get from it turns out to be bogus and you only get back on the main quest from something you learn after you abandon the worthless lead.
Some examples from Might and Magic games:
Might and Magic 6 - Control Center. Enjoy fighting hundreds of robots armed with blasters. Plus, not only can they break your stuff, but the aptly-named Terminator Units can Eradicate you.
Might and Magic 7 - Eofol Tunnels. Filled to the Brom with Medusae and Behemoths. The worst part? You can't do an totally invisible run because of a jump that requires the Jump spell, which still breaks Invisible.
Also from Might And Magic VII, perhaps even more egregiously, is the Titan's Stronghold. It's a dungeon loaded with dragons and the eponymous titans, who are nigh-impossible for anything but and endgame party to deal with (you'll stop by here much earlier than that). The only feasible way to get through to retrieve the MacGuffin within was with the master-level Air spell 'Invisibility'. The purpose of said MacGuffin? To allow your Archers to recieve their final promotions, which in turn allows them to learn master-level Air magic.
If you're doing the second Archer Promotion Quest so that your Archer can use master Air Magic, either you're doing something wrong or you can already kill whatever that place can throw at you. Probably the latter, as the former would require you to not have a Wizard or Warlock/Arch Druid in the party and not be compensating for it somehow.
Lands of Lore: The Throne of Chaos has the dreaded White Tower. The first floor's music can cure deafness, the second floor is puzzle-based, BUT the third floor features neverending waves of powerful ghosts who can phase through the walls, attack you through the walls, and will keep surrounding you easily, making movement in any direction impossible and death inevitable. One LPer tried to deny existence of the White Tower, refused to go to the White Tower, and then denied being in the White Tower.
There is a way to make dealing with the ghosts quite a bit easier using Vaelan's Cube. It even restores mana when used on a character after killing a ghost with it. However, actually bringing the Cube along to the White Tower in the first place counter-intuitive, as it has to be used to enter a town near the Tower (which destroys the Cube), and your business in the Tower cannot be completed without first visiting the town. However, everything you need to do on the third level of the White Tower can be accomplished before that.
Counterintuitively, you can use the Vaelan's Cube in the weapon slot. This means never losing a single cube, having multiple cubes to fight level 3 of white tower even after unlocking Yvel city.
Lands of Lore 2 has the Ruloi Citadel as the most irritating level by far. Much of it is wide open area, and the only enemy around (apart from the boss) is annoyingly fast, flies, and attacks you only with ranged attacks. One of the said attacks raises pillars of energy next to you, and a couple of seconds touching them will easily kill you even at the highest level. And these flying enemies like to retreat back to cubbyholes high up in the walls to heal themselves up. At least the enemies don't respawn. If the fighting isn't annoying enough for you, much of the level requires you to jump up and across narrow ledges, and falling too far will kill you in this game.
The very first level of Fallout 2. You build your character, expecting to use guns, to be handed a spear and told to go kill dozens of giant ants. To boot, the only medicine hurts your Perception (and ability to hit), you have to blow up a door and when you think it can't get any worse, the boss of the level must be fought hand to hand. Betcha can't guess what the bosses specialty is, can ya? Did I mention that traps are all over the level?
You don't have to kill the ants and scorpions, just make it through the level. And if you're a diplomat build (and you make it that far) you can talk the guard out of fighting you. I think a build type can steal the key, but I'm not sure about that one. You can also "cheat" in the fight by dropping your spear before talking to the guard, then picking it up during the fight and stabbing him. Still, it's a sign that some builds are better than others.
Each of the three premade characters has an easy way to beat the guard: you can fight him, convince him, or just steal the key. Now, if your three tag skills are Energy Weapons, First Aid and Gambling... good luck.
Then there's the Wanamingo Mine. Located in the settlement of Redding, it's available early and clearing it out is required to earn some potentially large monetary rewards. Unfortunately, the eponymous wanamingos are numerous, resilient, and hit hard, and their queen is even worse; a low-level character will be slaughtered. As will a mid-level character, and probably a high-level. Really, now, the best bet to doing this is to have a suit of Power Armor, and for most, by the time that happens, the Chosen One will be so rich and powerful, that the money earned won't mean anything anymore.
Old Olney is one of the easiest areas of the game. Just use a Dart Gun. The sewers are marginally more difficult, because you can't outrange the inhabitants. The Deathclaw Sanctuary is much, much harder, since you're fighting in tight corridors and the Deathclaws there can ambush you.
That's actually not so bad if you've got the YCS/186, anti-materiel rifle, or the fully modded holorifle. Dead Wind Cavern, on the other hand, is an absolute nightmare. It's even worse than the Deathclaw Sanctuary, although you do get the blessing of night-vision chems.
Really, any high level critical based weapon and a little stealth will work, provided you clear the entrance decently. Most Deathclaws will fall to one sneak attack and the Deathclaw Alpha Male will die in two. Or you can glitch the game physics and stand in a location where you can kill Deathclaws, but they can't kill you.
There's also several very convenient sniper perches in the Quarry. As long as you can clear out the two or three Deathclaws that surround it, Quarry Junction becomes a mere exercise in patience.
Also in New Vegas, Vault 34. Armored Feral Ghouls, confusing labyrinthine design, and several underwater areas are annoying enough, but the entire place is also irradiated, so good luck if you don't have tons of Rad-X and Rad-Away.
On New Vegas, the ENTIRETY of the Dead Money DLC. To start off, you're stranded in a dark maze-like city with NONE of your equipment except for some food and a holorifle with only 20 shots. The ghost-like enemies you find will just get back up if you shoot them, there are large sections of the city with poison gas that drains your health quickly, and there are barely any stimpaks or beds around to heal yourself. It gets slightly easier once you get to the Sierra Madre casino (mostly because there is an easy to find supply room with Stimpaks, ammo, some armor, and a couple police pistols)...but then you run into holograms which you obviously can't shoot but can kill you in a second if they see you. And that's not getting into the speakers all over the resort and casino that cause the bomb collar strapped to your neck to explode if you hang around them to long, killing you instantly. It's all worth it though for the end where you can murder the guy who locked you here in the first place.
Fallout 3's Point Lookout is That One Expansion Pack, being populated by super-tough tribesmen and mutated hillbillies with weapons that are haxed to bypass damage resistance. Especially the first quest at the Calvert Mansion, where you will expend your supply of Stimpaks like popcorn. Save Scumming is mandatory.
Back in New Vegas, another DLC. The Lonesome Road DLC gives us The Courier's Mile. Ground zero for a nuclear missile, radiation levels can climb above 25 rads per second, and it is filled with Irradiated Marked Men — which practically require one hit to kill due to the radiation healing — as well as Irradiated Deathclaws which deal radiation damage. The one good thing? The deathclaws have zero damage threshold and resistance. Not that it matters much since they'll still have 500 health, at minimum.
Diablo II: The Flayer Jungle. Let's see... massive randomly generated maze-like area which you'll probably have to explore every bit of to find both objectives (one being required to beat the game) brings on the tediousness, and the Fetishes that the area is named after bring the pain like none other. And... just read the entry, remember that groups of these monsters are all you're going to be running into.
Even worse is the Flayer Dungeon. Claustrophobic, ugly, full of traps, poison, exploding Fetishes and giant sea monsters that you can't hit properly. Unfortunately, you need to complete it. There is also the Swampy Pit, a second Flayer Dungeon that is non-mandatory. No one ever goes down there. Ever.
Then there's the Durance of Hate. It's not too bad in Normal difficulty but in Nightmare and Hell the level area is greatly increased into a huge sprawling maze of corridors, also inhabited by those exploding Fetish dolls.
There's the Maggot Lair in Act 2. Three levels of narrow single file tunnels with glitchy unresponsive slime doors, players getting stuck all the time in the narrow passages, then throw in the those lightning enchanted scarabs that everybody loves for good measure. And when you meet the boss, it takes so long for the room to load up that by the time you do, everything in the room has killed you during the lag.
The Arcane Sanctuary presents you with four paths at the start, only one of which leads to the Summoner and the portal to the Canyon of the Magi, meaning that most of it is unnecessary. This wouldn't be so bad except for the fact that it's a maze of bridges with lightning traps, Ghoul Lords that can cast powerful spells across the platforms, and ghosts that can fly over the space. The worst part is that this is mandatory to enter the Canyon of the Magi, and it's often difficult to get a group. to go in here.
Although Arcane Sanctuary is part of most power-levelers setups, 2-15 in tristram then head to arcane sanctuary more or less.
The Sorceress isn't the only option, either. A Barbarian with a few resistance-enhancing items and several points in Leap Attack can clear almost all of the gaps and maul the crap out of the spellcasters quickly.
An old one, but have to rant. The 4 Jewels dungeon in Legacy of the Ancients. go down seven levels worth of "everything has double the hit points and wants to kill you," booby-trapped chests, shitloads of traps, and the final level is split into four parts, leading you to climb back up, walk around more of the maze, drop back down, get treasure, and repeat. Oh...and the fact you have to climb your way out of the dungeon you've already plundered? VERY annoying.
Uplink had the LAN levels, which threw a LOT of people. Though it was fixed in a patch, certain LAN levels (they're randomly generated) were Unwinnable by Mistake, you needed one hell of a computer just to competently attempt them (at minimum, you generally have to run 3 bypasses and usually almost all of your LAN tools, plus the standards like trace tracker and password crackers/decyphers at proper moments. If you never learned how to manage your processes in that game before a LAN popped up, you learned then.), and what's worse is that logging into the mainframe always alerted the syasadmin to your presence, starting a countdown to get the job done, which was a real killer if the mainfraime was right next to the main gateway, giving you about 20 seconds to crack the password/encryption, get into the system, complete your mission, and log out before you get booted by the sysadmin.
Battle Arena. You have 1 minute to defeat a random monster with difficulty scaling up. The catch? The arena is a 3x3 square. To win a single battle, you need to win 3 fights on 3 squares so they form a line, tic-tac-toe style. There's a minimum of 250 battles to complete the quest. You're allowed only one combatant and the rest of your party is automatically locked-up. While Battle Arena is completely optional, but if you skip it you'll be missing out some very good rewards.
For those who are truly sick of the Battle Arena, there is a mod that will allow you to bypass the fights but still get the items.
Felwood. Didn't put any skills points in Wildneness Lore skill? Good luck finding your way around this trap-filled maze with identical areas.
Players of Planescape: Torment have found various parts of Curst to be the scrappy part of the game. From the daisy chain of treacherous quests, to the prison break of an angel beneath, to the warzone Curst becomes on returning.
Curst, beyond the extreme combat emphasis compared to most of the rest of the game, also is worse because of the Guide Dang It aspect. It is possible to rest in the prison, but only through dialogue through an NPC who only offers the option if you talk about completely unrelated topics with him. In which case, you could just spam Cloudkill. Of course, if you didn't think to buy Cloudkill yet or bring someone capable of casting it, that's tough because you can't go back until after you defeat this area.
Ravel's maze, although the location of many Crowning Moments, also features the toughest and least avoidable fight up to that point in the game. Immediately following the Boss Battle, shades pour into the maze, preventing players from recuperating and saving.
There are a couple of things that can be done to make this area a lot easier. One is to make sure you do some serious grinding and complete as many sidequests as possible before going. The other is to spam Morte's Litany Of Curses ability at Ravel until she fails her save, stopping her from casting spells and making the rest of the battle much easier.
The entrance to the Fortress of Shadow, is dark, disorienting, and crawling with greater shades which the Nameless One has to face alone. Some builds have no choice but to run like hell, dying many times in the Trial-and-Error Gameplay of finding the correct triggers to get past it.
The Nameless One's maze. Finding the exit is nothing short of a Guide Dang It. Fortunately, the whole maze is optional.
The Modron Maze. Having fun navigating in a 8x8 maze (that's around 64 rooms, depending on the Randomly Generated Levels) full identical rooms.
Dark Souls, being Nintendo Hard, has quite a few painful levels, but the worst is the lower level of Blighttown. A swamp that slows you down and quickly fills up your poison meter. Enjoy burning through your Remedies and Purple Moss Clumps. To make it worse, the Rusted Iron Ring, which nullifies the slowdown in the swamp, is hidden in the Undead Asylum, which is a massive Guide Dang It to reach.
Another infamous section of the game is the Anor Londo Archers. Despite Anor Londo actually having a couple dozen or so archers, everybody who's played the game knows which two I'm talking about. They're perched on a ledge on the other end of an enormous bridge, armed with Dragonslayer Bows that deal huge Knockback. Even if you get across the bridge, which has guardrails, you have to fight them on the ledge, which does not. They're even on opposite sides of the bridge, meaning you have to put your back to one to fight the other. It's so hard that the easiest way to handle it involves messing with the AI of the Silver Knights to make one of them walk off a ledge.
Elder Scrolls Arena: The tutorial dungeon. Where to begin? You're in a HUGE dungeon, thieves will appear and one-hit KO you if you loiter too long in one spot) Good luck trying to find the shift gate while fighting off hordes of rats and goblins which whittle away your life, and if you try to rest chances are there are multiple enemies nearby you have to kill first which are hard to even find. Did we mention this is the tutorial level? Todd Howard head designer for later games such as Morrowind and Skyrim admitted he attempted this dungeon 10 times and never got through.
Chapter Four of Paper Mario: The Thousand-Year Door starts off relatively simple... and then Doopliss steals your body and leaves you as a shadow. Now you have to run back and forth from the tower to the town, and back again, multiple times with only Mario (and later Vivian)... but the enemies (already a bit tougher than usual) don't get any easier. And you can't go back to Rogueport, either, so if you went in unprepared, tough break! It doesn't help that one of the most frequent enemies in the chapter has an attack that can put you to sleep if you don't guard properly (which will likely happen often). Then when you end up going back to Creepy Steeple, you have to go through a room with a bunch of Buzzy Beetles and Spike Tops. Buzzy Beetles could at least be flipped over by jumping on them, but with no Spike Shield badge yet, you were out of luck with the Spike Tops. And 4 defense means that unflipped, you'd need to have an attack-boosting badge just to deal any damage with the hammer. Nope, no POW Blocks for sale at the Twilight Town store, either. Hope you've gotten really good with Earth Tremor (which uses up about half of your star meter)...or got the Quake Hammer Badge.
The original Paper Mario is pretty tough in general. Some of the areas most annoying to get through are Shy Guy's Toybox, mostly due to the amount of different types of Shy Guys. The Pyro Guys, who can set you on fire and have rather high attack for this stage, and the Spy Guys, who can knock off some of your abilities. Lavalava Island is also pretty annoying to get through. All the different plants, most of which can poison you and the search for those Yoshi Kids. Also, the Crystal Palace is a bit irritating to get through. The saving grace for the last is the funny moments with the absolutely inept Duplighosts.
Riverside Station of Paper Mario 2's chapter 6 was a bit annoying to get through. The enemies are pretty tough and that damn garbage chute puzzle.
Mario & Luigi: Superstar Saga. Joke's End kind of defines this, as it's long, confusing, and an ice level with creepy and annoying music and teamwork puzzles. The worst part is the fact that you spend most of the area being split up. In the Mario & Luigi series, only having one brother severely gimps you, preventing you from using Special Attacks or reviving if you get knocked out. Since the enemies in Joke's End are very tough, you're probably gonna spend half the level running from every fight you see just to stay alive. Unless you grind endlessly once you get the bros back together, you'll enter Bowser's Castle severely underleveled.
Teehee Valley can also be considered this. Having to control Peach who wanders about aimlessly just WAITING to be kidnapped by the Gritty Goombas is certainly no day at the beach. Especially during that damn spin jump puzzle. Your switching of high jump to spin jump has to be QUICK and PRECISE, lest you fail. Then, if that isn't bad enough, you have to time your spin jumps along with PEACH, meaning that if she strays from the screen, she'll get kidnapped and you'll have to do it all over again. And you will. Again, and again, and again.
Not to mention when you return to Teehee Valley aboard the S.S. Chuckola there's that bleeping red and blue barrel mini game. A timed sliding puzzle where you have to get 6 barrels lined up ten times in less than 200 seconds? No thank you.
Heck, you won't even be at the first major boss in this game when you do the first of many hair-pullers of the game: The Border Jump. To get into the Beanbean kingdom, you have to jump over a rope that varies in speed. Seems simple, but for some it's really not. Oh, you're using an emulator where the keys are reversed? Good luck with that...
Mario & Luigi: Dream Team has Dreamy Somnom Woods. Why is this place annoying? Well for one thing, it's a gigantic maze based around a tree, with a puzzle right at the start that can easily confuse anyone who doesn't think to look around a bit more before progressing. It's also got quite a lot of easy but somewhat annoying enemies, and comes capped off with That One Boss at the end of the dungeon... and That One Boss at the beginning (to enter you have to fight Pi'illodium, to exit you have to fight the Zeekeeper, at least the first time around). It has really nice music though.
If you decide to tackle the Milky Well dungeon in EarthBound from the moment it becomes accessible, watch out, as mushroom enemies roam the grounds, capable of inflicting the Mushroom status effect, which functions as a combination Confusion + Interface Screw effect, leaving you susceptible to the attacks of the other difficult enemies roaming the area. Thankfully, the boss at the end is easily handled if you have either certain PSI or items. note PSI Flash Beta. If you don't have it, pray you have Fire Beta, Freeze Beta, and saved Jeff's Big Bottle Rocket. If not...
Don't forget the mines. Basically, you have to find five giant moles. Each one is similar and will take some sort of magic to defeat note PSI Freeze Gamma. However, the place is a maze, teeming with Ropes (tie up your characters and waste turns), Mad Ducks (drain PP), and, worst of all, Thirsty Coil Snakes and Gigantic Ants (loaded with poison attacks).
Peaceful Rest Valley, anyone? Every enemy is a Goddamned Bat or Demonic Spider: the Mobile Sprouts with the ability to make more Mobile Sprouts as well as heal themselves and suck away your PP; the Li'l UFOs and Spinning Robos that can give you colds; and the TerritorialOaks... If you face two of these four at the same time, you're in for a world of hurt. Thankfully, the game gets much, much better after this awful level.
How about the department store in Fourside after the lights go out? You've temporarily lost your primary offensive PSI user and the store is choked with Demonic Spiders. Getting massacred by records and coffee cups never ceases to be humiliating. You'll likely need revival items to get past it the first few times through... catch is, you can only buy them in Saturn Valley, which requires you to take the bus to Threed and walk through a rather long path to the store there. Then go ALL THE WAY BACK.
And then, almost immediately after you're hit with the almost-as-tough Moonside, which you can't leave until you figure out.
The segment in between trapping all the zombies in the tent and reaching Saturn Valley is a nightmare. You have to go through the Threed tunnels, which contain only three unique enemies barring the boss, but the Zombie Dog is very powerful and the Zombie Possessor is one of two enemies in the whole game who can possess a character with a Tiny Li'l Ghost, which either attacks you for 1-10 damage or stop you from attacking for one turn. The boss, the Mini Barf, is nothing special, but then Grapefruit Falls comes, where you have to make your way through multiple enemies that can put up a fight and possibly deal with the Tiny Li'l Ghosts preventing a critical character in whatever strategy you're using from moving for a turn, letting the enemies brutally murder your party. The kicker: there is no phone in either of these areas. If you die, you start back at your last save point, most likely the Threed Hotel, with the only bit of mercy being that the Mini Barf isn't there any more if you decide to continue.
Mt. Itoi in Earthbound Zero personifies this trope. How bad is Mt. Itoi? You could conceivably rename Disappointing Last Level to Mt. Itoi Wannabe, and it'd probably personify the trope better. It's not only long, but it swarms with Demonic Spiders that give minimal experience when defeated and the random encounter rate is beyond sadistic. In fact, when asked about the difficulty of Mt. Itoi, the game's creator said that he just wanted to finish making the game and didn't bother to balance it. And it shows.
MOTHER 3' Back Beat Battle Hard and Ode to Ancestors, 8th movement are perhaps two of the hardest songs to combo in the entire game, the former due it its erratic rhythm and time signature, and the latter because, it being a medley of classical songs (whose tempos are a bit hard to find if you don't have an ear for such music), it changes tempo constantly.
You forgot 'Strong One'. Oh my God, Strong One. Listen to that. Now imagine trying to COMBO that. It does NOT help that the only consistent enemy who uses this melody is also the SAME enemy that has a one-in-128 chance of dropping a VERY powerful item. If you're looking for that item, you will learn to hate this song.
Learned to hate Strong One yet? Here's the Masked Man version. As if the original wasn't hard enough, this one has the very last portion of the refrain sped up, likely JUST to screw with your combo.
MOTHER 3's ocean level. You've got to make your way across the bottom of the ocean to Tanetane Island. Obviously, you can't breathe underwater, so you have to get air by kissing mermen. If you run out of air, you wash up at Tazmily Beach again, and have to do the whole level over. In addition, there's also a good deal of excellent items down there (including an Awesome Crown for Lucas) that you can only get by going through long caves with nowhere to replenish your oxygen supply, meaning it's pretty much suicide to get it. Also, there's a surprise Heads I Win, Tails You Lose battle at the end.
Let's not forget the Stonehenge Base from Earthbound. It's a long base, the monsters are a step up in difficulty from anything you've faced, and the 1-in-128 Sword of Kings is here. It's difficult even if you're not trying to pick up the sword. And, if you finish the boss of the dungeon, say goodbye to searching for the sword.
At least if you're patient enough to grind yourself stupid looking for the Sword of Kings you'll become so over-leveled that you can practically sleepwalk through the rest of the game without much of a problem.
Golden Sun 2 has Air's Rock, the rest of the rocks are annoying, but Air Rock takes the cake, it is hard to figure out even WITH a guide.
To elaborate: The game doesn't even give you a reason to bother with Air's Rock, as it doesn't tell you that an important and plot-centric skill is located there. When you finally do tackle it, you start out solving a bunch of annoying maze puzzles that require you to use a PP-draining skill over and over again. Air's Rock is near the beginning of the game, so you have very little HP and PP, hardly any good equipment, and the enemies are a significant cut above what you've seen so far. After the mazes, you get to climb up the mountain, solving annoying platform puzzles and engaging in a lot of Trial-and-Error Gameplay on the way. When you reach the top, you've likely spent nearly as much time as you did in the previous game's final dungeon. But, reaching the top isn't the end of Air's Rock; horrified, you soon discover that you're only one third of the way done. You then venture inside the stone, and proceed to make your way down, level by level, to the heart of the mountain, solving annoying and repetitive block puzzles along the way (the enemies have got an upgrade at this point.) After you finally reach the heart of the mountain, a process that takes about as long as the climb up did, you've got to go back to the top level and go down a different way this time, using the newly revitalized tornado machines to worm your way through previously inaccessible areas. Only at the end of this segment, which is also about the same length as the initial climb up the mountain, are you done with this horrible, horrible level.
To add even more insult to the injury if you payed the first game, the plot-centric skill that you learn here was one you were taught for free in a town in the first Golden Sun.
The Sea of Time. Fuuuuuuuuck. You're navigating currents, with your only clue on what to do being the song from Yallam that Yepp wrote. The controls are irritating, it's difficult to get out of the whirlpools once you're in them, and the music is little more than ominous drums, which quickly goes from 'atmospheric' to 'SHUT IT UP'. Also, one slip will send you back to the beginning. Did I mention it finishes with That One Boss? And if you didn't have the foresight to save, you're going through the Sea of Time again?
In Golden Sun: Dark Dawn, Otka Island. Just Otka Island. You need the Sol Blade to get inside this hellhole, and the encounters inside can prove it if you've been slacking in your Level Grinding. But that's not the worst part. The damn thing is a ginormous maze, spanning several Zelda-esque square rooms. That's not the worst part, either. The auto map is absolutely useless when it comes to finding your way, simply showing the image of the room from above with a giant ? in the center. There are four good chests mixed up in there, meaning that without an actual map, you will invariably get lost. That's STILL not the worst part. The worst part is after all that madness, after referencing your position, checking your map in triplicate, and finally getting to the end, you are greeted with a summon tablet... guarded by the Ancient Devil. Get used to the soft reset command, and I hope you don't have Sveta on the front line when you commence combat. I really hope you don't. (To clarify, Ancient Devil has an attack called Demon Sign, which turns one of your active party members against you. If Sveta's on the field, he'll almost certainly use it on her. Suddenly, all of Sveta's awesome attacks and healing spells aren't so much fun anymore...)
The first one has Altmiller Cave. Not only is it long and filled with nasty enemies, but it's also completely dark. The only light you get is from torches and the standard little bubble around yourself. You either have to bumble around rock mazes, trying to remember where you have and haven't been, or waste Ivan's PP and use Reveal constantly. And, to rub salt in the wound, the bottom floor has an infuriating puzzle involving memorizing a riddle you heard at the start of the dungeon, unless you cheat and use Reveal to see the colors of the rocks.
Another aggravating part is Lemekan Desert. The dehydration mechanic wouldn't be so bad, if your characters would just shut up about the heat. It also doesn't help that the boss of that area, Manticore, is the first boss that can move twice per turn, so you're not likely to be ready for it.
Fossil Fighters has the BB Brigade base. It's not annoying because it's long (it's rather short, in fact). It's not annoying because it's complicated (there's no real puzzles to speak of). It's annoying because, in a game where all the battle encounters up to that point have been optional, it's full of aggressive opponents who will swarm you and constantly force you into mandatory battles. They're not especially difficult, but they're nigh-on endless.
Other JRP Gs
The Tower of Zosma in Baten Kaitos, which is a very good argument for killing anyone who suggests putting a Block Puzzle in a video game ever again. The way up isn't horrible, if you're good at these things, but Mizuti's quest...
The very short passage through the Outer Dimension (right after you meet Mizuti) is like this. Lots of skill required to navigate, recognize the enemies and time your hits, and at least three unique Magnus involved... which are photos.
Baten Kaitos Origins has Tarazed. It's an Eternal Engine in which about half the rooms look exactly the same. Oh, and it's huge - the biggest level in the game by far. Thus an already long level is stretched out even further by the player having to find a room to use as a landmark at regular intervals. Did I mention the one-way paths? Or the fourmaze rooms? Or the Machina Auto-Turrets, horrendous Demonic Spiders that swarm through the halls? At least the music played there is among the best in the game (which, for this game, is saying a lot).
The Nekkar Quietlands. It's full of Demonic Spiders and pit traps that greatly complicate a would-be simple layout, and they're impossible to see coming unless you already know where they are, leading to lots of Trial-and-Error Gameplay. And when you beat it, you're given That One Sidequest, which requires you to stay much longer than you did in beating it in the first place.
The final dungeon of Suikoden V is a combination Scrappy Level and Guide Dang It; when you enter it, you're forced to choose three full battle parties of six members, and have to constantly switch between them. If you don't have eighteen party members up to snuff? Too bad, you can't leave. This can make the game nigh Unwinnable unless you know it's coming ahead of time, or obsessively create backup saves.
Not quite, you CAN leave the dungeon if you talk to your party-changer at the entrance, but it's still a pretty nasty place. And sadly, the best area in which to level up is the area before it. And if you want to change your party you can't just warp back to your castle until you go to the final dungeon, which sends your party changer back there when you leave said final dungeon.
The Deep Twilight Forest also qualifies, especially if you want to get all of the treasures. The ruins part is not so bad, but the forest part beforehand can be frustrating since many of the paths are obfuscated. Deep, indeed.
Speaking of Shin Megami Tensei dungeons named Karma, the Karma Palace from Persona. Full of pit traps... most of which eventually take you back to the entrance... but one sequence of which is necessary to trip exactly right in order to actually reach the boss. It's not truly a Guide Dang It, but one sure helps.
The Alaya Shrine. Harder enemies than any prior dungeon. Several types who are immune to conversation. Several with either area instant kill attacks, or status ailment attacks. None of this would be overly problematic...except you only have two party members.
The PSP remake of Persona 2: Innocent Sin introduces a movie theater that has all sorts of extra dungeons in the form of movies. One of these is School of the Heart, Part 1, which is an incredibly annoying maze with rather powerful random encounters (around level 16; it's possible to get here when your party averages level 4). Some doors don't work, others do gobsmacking amounts of damage when you try to use them, and the ones that do work lead to minibosses which usually aren't too tough, but warp you elsewhere after you beat them.
Though all of Tartarus could count in Persona 3, the fifth block is especially annoying. It is mostly dark, except where multi-colored disco lights are thrown around. Not only is this difficult to look at, enemies onscreen (Shadows which are black) are nearly impossible to see until they bum-rush you. Better get used to using your radar.
Floor 7 of the Void Quest in Persona 4 is nothing but intersections that randomly throw you into different directions, so it's all too easy to have an overpowered Shadow ambush you. On top of that, the mandatory midboss is on this level, and skipping it will make you miss out on a key item needed to access the end boss. (Thankfully it's easy to backtrack to.)
If you rush into the intersections where the camera angle changes, you're going to get lost VERY quickly. But if you go in slowly and carefully, taking a moment to get your bearings after the camera shifts, it's a lot easier. It helps that shadows rarely move close enough to the intersections to rush you.
Shin Megami Tensei III: Nocturne seems to be out to get the player every time there's a dark dungeon. You NEED Lightoma/Light Balls, or you can't even see the map. Not to mention they usually have some crazy puzzle going on (the four Oni, the hills...)
Don't we all love the Diet Building? No, no we don't. Fake walls and doors that get you teleported away for being tricked...
Amala Labyrinth. The Cursed Zones are beyond frustrating. That and Dante tag. And the Invisible Walls. And the mazes of doors... Okay, EVERYTHING in it.
The Second Kalpa deserves special mention just for the fact that the whole thing is one massive Difficulty Spike. The first floor has a gigantic maze which is a pain in the ass on its own, but then you jump down a few holes and stumble into what seems to be a large, empty room. Hope you like navigating mazes with invisible walls! But the Cursed Zone there really takes the cake. You lose half your health every couple of steps you take, there's a lot of one way doors that exist solely to get you turned around, but it's the random encounters that'll really get you pulling your hair. The demons you fight here are level 65, at least, and know a variety of horrible moves (Dormina + Eternal Rest, anyone?). And you're probably around level 40 by the time you find this place.
The White Shrine. The doors teleport you, and using different entrances to a room will send you elsewhere. On the second floor, the doors don't teleport you (in fact, there are no doors), the floor does. To top it off, one must face GoddamnedPuzzle Boss Albion at the end of it. And it's worse if you want to find the reusable instant-death artifact.
Not to mention the 5th floor, which combines the darkness with the conveyor belts. You had better get the Visualizer main app...
And then Eridanus throws in rooms full of nothing but trap tiles, accessed through one-way doors, and an entire required area of teleport traps and another of pitfalls (and more one-way doors). Take the wrong pitfalls and you wind up at a part of the teleport maze that takes you back to the start of that! This is ignoring the encounters, some of which are the first to not have weaknesses (but can still hit your whole party - hard). Also, that new Visualizer App you just picked up in Delphinus? Doesn't work on the dark zones in here.
Grus has some purple forcefields that just decide to show up and block your path. Oh, and unlike in the other sectors, there's no way to get around it later - they're always there. And it turns out some of them disappear when approached, all of the ones that do that will be passed at some point... while the solid ones sometimes have a teleport in front to screw with you. If you're not staring intently at your automap the whole time, you will get lost. There's also a maze of one-way doors at one point, and finishes up with That One Boss.
The New Game + part of Grus. Where it's a trial-and-error linear path to a one-way door maze with Phase Shifting thrown in. And may the Great Will have mercy on you if you decide you want full map coverage, as you have to enter the same maze over and over and over... in every Phase Shift.
Horologium decides to take the mindscrew route: let's have the player walk across nothing. Seriously, there's no hint that you have to walk off the platforms (every time you do, it actually changes the map boundaries). And while you bumble around looking for the path, the Random Encounters bleed away at your health. And then the next floor has fire pillars pop up out of nowhere, which can't be turned off without a path to an elevator - surrounded by teleports. Keep in mind that said encounters have skills like Megidola, Ragnarok, Killing Wind... and you probably recognize the name Rangda from other games...
Horologium's 4th floor full moon puzzle. You'll be wandering around trying to find the right teleport, and then go in during thewrong phase.
The Paranoia levels in Majin Tensei II, You will be tearing your hair out because your human's walking distance is heavily minimalized except on Plains, Humans are necessary to occupy the enemy bases in most of the levels. Gee takes the cake though as most of the map is mountain and sand! Which means you will only be able to walk 1-2 squares per turn. Combine that with 3 demon generators near the end and 2 Pendragons near the start which has a large range of attack and you will be raging. The only saving point Gee has is that it has 4 regeneration panels. (2 near the start and 2 in the middle)
.hack// has a few of these. Chosen Hopeless Nothingness from the end of the first game is a major example, as it's 5 floors (the maximum), Goddamned Bats make up every single encounter here, and it has That One Boss at the end of it. Then there's Generous Bemused Virgin from the third game, which forces you to include a level 1 character in your 3-person party (whereas everyone else is level ~65 at this point), and has quite a few enemies that would be Demonic Spiders even without this handicap. The worst offender by far, however, is Reincarnated Purgatorial Altar. For one thing, it breaks the clearly established 5-floor dungeon limit rule to have 10 floors. For another, there's a ton of encounters in each floor, most unavoidable, and every encounter puts you up against a boss. Every boss fight in this game (except for the Cubia fights) requires Data Drain in order to kill, and abusing Data Drain can cause plenty of negative effects, such as stat problems. And that's if you're lucky—if you're unlucky, you'll actually lose experience and level down. If you're REALLY unlucky, you can even get a Nonstandard Game Over. And of course, Murphy's Law dictates that this is most likely to happen in floor 10, which will most likely cause your disc to be thrown into the wall. And the boss at the end of floor 10 is a Marathon Boss.
Rogue Galaxy, Gladius Towers. A pair of 8 floor towers with a ridiculously confusing overlapping layout that has you switching towers every second floor, with countless dead ends that makes the ingame map completely useless. And once you're done with one of them, you still have the other one left. At least the enemies aren't too bad.
The Gladius Towers were long, but at least the enemies were easy enough and no one can say the inside of the towers weren't cool to look at. The Leo King's Castle from the same chapter, however, was an absolute bitch to complete, as near every enemy in the castle and the path leading up to it were cheap (even by Rogue Galaxy standards) and the dungeon was nothing more than miles and miles of endless repetitive blocky walls. Capping this hellhole off at the end is a boss fight against the Mad Witch, one of the most mind-breaking difficult boss fights in the entire game.
Guardian's Crusade has the dreaded swamp level. Since you're still in the beginning portion of the game, chances are, your levels are low. This does not help when you combat enemies who almost always knows AND uses poison. Not only do they take a HUGE chunk of your life, they will also use Terror against you which prevents you from attacking. If it gets to Baby, it won't even be able to heal you. So now you're torn between trying to heal and stay alive before they do worse.
The Tombs of Amenti, available only on on Hard Mode. The entire place is a twisting mess of corridors filled with annoying obstacles and enemies by the truckload. Navigating the dungeon using the map is useless: you have to use a guide to find the two keys needed to summon the dungeon's boss, Akhetamen. And Akhetamen is no pushover.
The second game has the Palace of the Venerated Dragon. The battle arena for the light colored areas is a straight, narrow corridor that's made narrower by torches. In these arenas are ghost-type enemies, meaning they can't be hit by anyone except mages and archers, with high magic attack, and a wide attack range. The enemy leader, who you have to kill to finish the battle quickly, is on the opposite side of the corridor, with at least two or three of those ghost types between you and him, meaning there's virtually no way of getting to the leader without getting hammered by at least a few of their spells.
Breath of Fire III has the Desert of Death. A rather silly Insurmountable Waist-Height Fence is the only thing preventing you from skipping it, and a dialogue translation mistake will make it much harder for you to make it through unless you know the very precise set of directions that will take you through it. Additionally, if you wander there too long, and run out of the water canteens, your max HP lowers with every step you take until you either finish the desert or go to rest at an inn.
In Breath of Fire II, we have Memory Tower. It uses a very strange inversion of the Fog of War trope; it shows you everything on the floor you're on except the area right around you. Unfortunately, it defines "the area right around you" as about half of your screen, forcing you to memorize the exact layout of the place, which can feel quite maze-like in some areas. This means a lot of random encounters as you move around trying to get a clear view, which is exacerbated by the fact that you're forced to have Spar in your party, who is (depending on whether you got the Guide Dang It shaman power-up for Spar) either the weakest character in the game or second weakest only to Jean.
There's a level much worse than Memory Tower, in the form of Highfort. It starts off rather pleasantly with the fact that there are two beaches that you can use to get to it from your whale, and if you go on the wrong one, you'll encounter a Beef Gate without even realizing what you did wrong, since the other one is on the other side of the continent. Once you enter, say hello to the Point of No Return, followed immediately by losing three out of four party members. The one who is left is not the main character, in a game without Leaked Experience. Weren't using that character? Well, let's hope you didn't use that save point. Oh, you did? Then restart the whole game, and we hope you won't miss those 20 hours of work. Even if you were using that character, said character is something of a Glass Cannon, and there are indeed Random Encounters (and a boss battle) before you reunite with the party. And once you do, you are greeted with an obnoxiously large maze section with obnoxiously strong random encounters all throughout, some of which have the Death spell. On that note, so does the third boss of the place, which also halves all damage that isn't Holy elemental. The second one absorbs any elemental magic you use on it, and has a very nasty That One Attack in the form of Typhoon. And to get to this boss, you must first enter one of those three portals you see in front of you, with no indication of which one will work. Guessed wrong? Restart the whole thing! And the translators spelled two of the bosses' names wrong.
The original Breath of Fire had a land of dreams maze, where there were panels that, if stepped on, swung the entire map around repeatedly. Let me repeat that: the entire map gets rotated at high speeds. This might not be so bad if many of these panels were on single path ways (with no landmarks to tell which way is forward and which is back). Which means that you could, and would, probably be going back and forth for HOURS, trying to find your way forward. Additionally, the one shop in the entire dream world sequence leading up to aforementioned rotating maze has all the healing items mislabelled. Glorious.
Blue Cave in Quest 64. Twice as long as any other dungeon. The first third has a bunch of tree branches with the correct ways pointed but you explore the rest in case of loot. The last third is a large causeway maze to the other end. Skelebats are the in the maze.
Skies of Arcadia gave us Moon Stone Mountain, a long dungeon with powerful enemies that had floor tiles that could open up and drop you back to the beginning. The first couple tile sets are marked so you can tell which tiles will open up, but later sets trade the Xs and Os for triangles, so you have to guess. And then you get to the end and realize you forgot to get the moonfish, so you have to go all the way back again!
This annoyance is bolstered by one simple fact: If you want all the chests and 100% completion to get the "Legend" title, you HAVE to take all the wrong paths at least once. Being mildly obsessive compulsive has it's advantages.
South Ocean thanks to the occasional Graver Random Encounters. They can not only drain your health to heal, but have Eternum, which you only have one way to defend against at the time, which depends entirely on you using an absurdly rare random drop/chest item to teach Aika at least two of her (character-specific) special moves. And you'll have to use this move EVERY TURN unless you feel like having a party wipe, which at standard levels takes off a fourth of your technique pool for the turn.
Digimon World Dawn & Dusk versions have two very frustrating levels: Loop Swamp and Shadow Hell. The first doesn't have many strong enemies, but it involves teleporting throught whirlpools. Problem is, the whole are looks the same, the Random Encounter rate of the games is very high (and no Repels), and most missions on this place involves talking with multiple NPCs, which are a chore to find. Shadow Hell doesn't have whirlpools, but it's a very large area that looks the same, have many dead ends and the Random Encounters are not only frequent, but they have several Damage Sponge enemies.
And ElecMan's stage, which has invisible floors, trial-and-error battery puzzles, and infected programs which you can't tell from the regular ones until you talk to them, at which point they attack. However, the real problem in the stage is the timer— once it runs out, Mega Man stops healing after each battle.
MMBN2 has FreezeMan's storyline, which is full of endless backtracking, and the aforementioned QuickMan.
MMBN3 has, as mentioned above, any level where the Press program is needed, especially BubbleMan's scenario where you first get it. Don't forget the endless fetch quests, which are somehow MORE irritating in this game than in any of the others.
Even worse than Press is Energy Change. You need to grind up an absurd amount of Fire chips to be able to get through the first dungeon that mandates it, and said dungeon has 6 separate areas! It's slightly less hellish if you get the OilBody program, which, unfortunately, is found in that dungeon. The second part that needs it is about the same, but uses Water chips instead of Fire.
MMBN4 has the levels at Castillo and the point collecting, the Demonic Spiders in alot of areas, especially the Undernet and Murkland.
In Red Sun, you have Searchman's scenario, with a sniper taking shots at you periodically. The shots do 100 HP, are hard to dodge, and you've probably got around 400 by the time you've reached this stage. Do the math. In addition, there's Thunderman's scenario, in which you are cursed; what this translates to is your health dropping at twenty points per second, even during dialogue, and it doesn't stop until you find memory chips and bring them to a specific spot.
Blue Moon players have Metalman's scenario, in which you have to play an annoying minigame that requires a lot of precision timing, and Protoman's scenario, which is a PIXEL HUNT through the Undernet that misinforms you on one of the keys.
And for the universal stages, there's Videoman and Coldman. Video has you running through the Internet to pick up tapes with your controls reversed and panels that will send you back to the beginning of an area. Cold has you destroying transmitters as Lan's body temperature drops. If it goes too low, Megaman can't use any attacks except the Buster. To actually destroy the transmitters, you need to go through a string of virus battles, and then sacrifice a specific Chip in a specific code. Oh, and if you leave to go get the chip(s) you need, the virus battles come back.
MMBN5 has the Ship Comp, a water dungeon which you have to guide your current Navi through. While they are underwater they are perfectly fine until they run out of "cyber-air" (really!), at which point their HP starts dropping rapidly until you either hit a cyber-air pocket or exit the water. Oh, and there's random encounters the whole way, including while you're attempting to fight the currents that push you back and drain your air, and while you're trying to avoid the whirlpools that drain your air. Oh, and you had to do this several times before fighting the boss. And to top it all off, you had to come back here later in order to get some of the items that you couldn't collect if you wanted a 100% completion.
In terms of the Internet proper, End Area 1, 3 and 4 are all absolute hell to navigate. They consist mainly of labyrinthine passages that all look the same and have almost no landmarks (save the pagoda in the third area). On top of that, they're all notably larger than any area so far, and the third and fourth throw in one-way conveyors. What's that, looking for Larkman? Good luck finding the invisible path in the first area!
MMBN6 has the Aquarium Comp where you have to solve fish riddles via 'escorts', that's right! Not only do you have to figure out the correct key NPC for the very vague riddle, you have to escort him as well! And when you pick him up, sharks appear and you had to avoid them via a Pac-Man-ish minigame and some of the sharks more very quickly. If one of them catches your escort, he gets eaten and you'll have to run all the way back to him and start over, all with lovely Random Encounter with some annoying virues. And to top it all off, you have to do this again at the end of the game as part of the Boss Rush!
Mega Man Star Force 2 has the Bermuda Maze, which can only be properly navigated through with hints given from Hertzes. All well and good until they start outright LYING to you and you have to check the color of the stars displayed in the sky, making things even more jumbled and confusing.
The Loch Mess has you swimming around, digging for golden Mr. Hertzes. The clues as to where they're buried are painfully cryptic. And if you're even a fraction of an inch off on your digging spot, you're thrown into a virus battle with no reward.
The Whazzap Ruins are also extremely annoying. You have to direct Flame Hertzes to their pedestals, which is easy enough, but there's a robotic condor that will knock them away, forcing you to go BACK to get them again, unless you can duck into the shelters in time. And in the second area, you have to direct THREE of them at the same time.
Finally, there's Mu. You have to go through the wave road to collect runes that allow entry to the next part. After you get the runes, however, walls come up to keep you from going on, and some Murians are summoned. If you come into contact with one, you have 3 seconds to draw a specific pattern on it that appears for less than half a second. Fail, and you have to fight two at once. Oh, and you need to memorize the patterns on the runes you collected and put them into a specific order, otherwise it's Murians for you again.
The Phantasy Star series is definitely not without its horrific dungeons. A good amount of the ones in the second game come to mind, with Climatrol being the first one to really kick your butt. Wren's Cave in the third one will kick your butt, too, especially since you only have two characters to tackle it with.
In Drakensang there's the Moorbridge Swamp: the level is filled with undead and poisoning foes, is unusually hard to navigate being a swamp and all and contains the dreaded Harpies, which can wound your party to death in a few strikes. Another hard level is the mission in Grimtooth Castle, where you'll have to face tons of powerful orcs and ogres. The sequel has the Temple of Efferd, which is full of Giant Enemy Crab monsters (which, like the above-mentioned Harpies, can wound you pretty easily) but thankfully is a Bonus Dungeon.
In Lunar: Silver Star Story Complete the Crystal Tower counts as, without the Game-Breaking Bug, you're forced to go through the entire dungeon without weapons. It's made easier by the ability to use wands as magic items, but even then there's only so much they can do, and the game never tells you this option exists. You can also try spamming skills, but that's going to lead to a complete lack of SP pretty quickly. And Star Lights aren't cheap, especially in a game that has a fairly balanced economy (at least at this point in the game, where you're selling off anything you have just to get the newest armor for one of your characters).
The Grave Ruins Base in Mega Man X: Command Mission is home to a highly-annoying security beam mechanic. The beams are Color-Coded for Your Convenience: Red beams will throw a somewhat-difficult random encounter at you, yellow means it's about to turn red, and blue beams are passable. All beams are red by default. There are switches to turn beams to blue...but as you progress, they wear off faster and faster, to the point where the last switches only turn them yellow. Oh, and all doors in these rooms are locked while the switch is inactive. And then there's the Revolver Room, which can be moved with a pair of switches, except you're not told what combination of moves will take you to the next room, and other rooms lead to some pretty good treasure. Also, there are no teleport points in the middle of any dungeon. Meaning, if you go in and then want to go back to do some shopping, or check on the Deployment Center, you start at the very beginning of the base.
Breath of Fire IV gives us Fou-lu's tomb. Incredibly frustrating? Check. Monsters that are a step up in difficulty from anything you've encountered? Check. A puzzle that can permanently lower your HP until you rest at an inn? Check. And, for added level scrappiness, it's sandwiched in between the game's two examples of That One Boss - you fight Won-qu to enter, Won-qu being the hardest boss up to that point in the game. However, I and II show up at the end of the tomb to relieve him of that title.
Opoona's Dome Ruins are a particularly nasty dungeon. The dungeon itself is longer than the other dungeons so far, and can only be navigated through a series of sinkholes and elevators that's confusing and not always intuitive. Many of the enemies are outright Damage Sponges, even with the magic attacks your new party member brings. Oh, and there's a chance that you'll encounter a brutally difficult random enemy in the room right before the boss, likely defeating you and sending you all the way back to the city. The boss itself is no slouch either, having multiple hearty enemies and healers.
The mine in Lufia II's DS remake for one reason: That Minecart minigame, which has very few check points and isn't easy what so ever. If not for this, the Mine would be a very nice introductory dungeon.
The Inca Ruins in The Sword And The Fish. They are long (VERY long) and the random encounters enjoy a dramatic increase in strength and frequency in comparison to the previous dungeons (not to mention that they take a loooooooong time to kill. I'm talking three-five minutes per battle, which occurs practically every ten steps). Even with Presto Mundo's Me Love Me Life tech skill, this place is still frustrating.
There are two real contenders for this in Last Scenario. One is Archaeopolis, which is full of extremely slow-moving platforms that aren't synchronized, so you often have to wait for some time before they line up right. Its only redeeming factor is that it's short. The other, the Underground Waterway, is frustrating for a different reason- you can't backtrack and the random encounters are hard, so if you didn't bring enough supplies, you're screwed. Oh, and there's a Wakeup Call Boss at the end.
Andau's Castle, the first dungeon of Master Of The Wind. One area has you trying to guess how to drop into the second floor, which is locked from the inside. You can jump into a giant pit by swinging off the ropes hanging from the ceiling, but in 90% of cases this drops you on a cracked floor, which dumps you back onto the first floor (and if you're unlucky, you'll land on another cracked floor). The solution? Move a rope that doesn't show any signs it can be moved - and which is almost off-screen from the spot you find its switch! - and swing on the new path to a switch that removes the slide covering the right hole. That's right, none of the possible jumps are correct. It's like they were trying to find the worst possible way to start a game.