Not really That One Level per se, but the desert you must cross to get to California in Oregon Trail II gets on many people's nerves.
Ditto for that game's river rafting minigame, which is much tougher than the original's and requires a lot of trial-and-error and dexterity with the mouse to pass, especially if you choose to shoot the rapids. And the Sublette Cutoff, which is unavoidable if you're a Greenhorn. If you forgot to bring canteens and/or water kegs, your party WILL die of thirst.
Brain Age 2's unskippable connect-the-dot images and acrostics. And when more than one person is using the same game card, drawing a picture of something the game tells you to. All of the above includes getting upstaged by the game proving it's better than you. Because you are facing aprofessor.
For people with OCD/impatience, the number memorization game within the trademark Brain Age-checking system. Sure, it's supposed to help your memory, but many just restart their DS when they get to it then re-take the test until they get one without it, because it's too frustrating to complete, but too easy to cheat at by writing the numbers down somewhere.
The crossword puzzle from Jump Start5th Grade. You're supposed to go through the museum to find the answers, but this tends to take forever (And as many have said, it tends to be pretty well-hidden. Made worse by your parents who could have set a time-limit...making it unwinnable).
Freddi Fish & Luther's Maze Madness gave us Level 24, an incredibly long and tedious level compromised of three rooms. One of the rooms in particular is filled with opening and closing leaves, that will only let you through when they feel like. This makes the level drag out for as long as possible.
SPY Fox in Cheese Chase includes Level 75, "Carnival of Clouds." You navigate through narrow passages of rollercoasters, all of which are one hit kills. If you do so much as touch the corner of one of the tracks, it's over. This is often the one level where people use the "Go slower" junior helper.
Spy Fox in Hold the Mustard has the passageway levels. Compared to the rest of the game which gives you a sky to fly around, the passageways are narrow tubes, and thanks to the lack of Mercy Invincibility, walls are almost always one hit kills, unless you get lucky and somehow manage to escape before your health drains (and even if you do, you'll still probably have only one hit left). The microscopic enemies certainly don't help matters, considering they also knock you far back, commonly into the walls. This is all bad enough; the fact that there are sixteen of these in succession instead of the usual eight, it's one heck of a ride. Sure, you can break up the action a bit by going to the secret Atlantis levels midway through, but they aren't much better.
Putt-Putt & Pep's Balloon-o-Rama has Level 108, which has balloons encased in a line of pinwheels and bumpers. For those who don't know, it plays like Breakout, except there is gravity thrown into the mix. The bumpers will be sure to keep you out of there though, and the pinwheels are supposed to send you in a random direction, but more often than not they just act like the bumpers. This makes getting the balloons they are blocking dang near impossible. You will be playing this level for a loooong time before you finish it.
Putt-Putt & Pep's Dog on a Stick has a level toward the end where you are traveling along one-square wide paths, with four hedgehogs in your way. This is a Q*Bert styled game, and the hedgehogs are the fastest enemies in the game, so they are a giant pain to dodge. There are also switches all over the level that add additional squares to help you some, but often the hedgehogs will hog the buttons and just keep switching them on and off as if to taunt you. Getting through this level without the unlimited lives junior helper is a big pain, unless you exploit a glitch that lets you jump through enemies with the proper timing. And even then, it hardly helps because you'll probably just land straight into the inevitable hedgehog that was trailing it.
Moose's entire scenario in Brain Dead 13. It starts when you enter Moose's room and, immediately on entering it, you notice a stone football getting thrown into your mouth if you don't avoid it. Once you get past that football, you have to dodge another football, along with Moose's grabs, shoulder charges, baseball bat attacks, being flung by a basketball net as a catapult, and the grab from below his head, all in the first quarter of this scenario (followed by a lot of Deadly Dodging of the lightning rods in the second quarter; finding a way to destroy Moose in the third quarter; and dodging Fritz as usual in the final quarter)! Failure to avoid any of these attacks in the first quarter of this scenario will send you all the way back to where you entered the room in the split-second that the same stone football is getting thrown into your mouth again!
The first mission of the MechWarrior 3 fourth campaign. This is the onlyTimed Mission, in which you have to fight through a couple enemy patrols and catch up a train. By this time, there is a good chance you have discarded the lighter Mechs in favor of the slow 100-tonners, the timing is very tight, and the enemy patrols have guns which can knock down even the heaviest Mech.
Remix II, Stage 1 in NES Remix. The first section is a simple "Enter the cave" scenario from The Legend of Zelda, and is easy to get past even with the blue Lynels and the constant screen blurring and unblurring. After you enter the cave, the second section unexpectedly changes to Donkey Kong, except instead of playing as Mario, you're still playing as Link, who can't jump or use his sword (or the two Hammers in the level). The barrels fall in such erratic patterns that it becomes a Luck-Based Mission to get to the top.
Hitman 2 has a level called Hidden Valley, where the sole objective is to get from one end of a valley to the other, evading swarms of ninja guards. This isn't actually all that hard in itself. However, the highly trained ninjas apparently do not have the slightest understanding of basic road safety and have a habit of getting themselves run over by the truck convoys going through the underground tunnel. This would invariably result in the body being discovered and the alarm being raised, ruining the player's chances of getting the top mission ranking of Silent Assassin through no fault of their own. This would happen about four times out of five and could happen at any point in the mission, even when you were just seconds from reaching the exit. The only solution was to just keep trying again and again and hoping you got lucky.
The Motorcade Interception mission of Hitman 2 is an exercise in hair-pulling because of the way the civilians are handled. Their starting positions and walking routes are randomized, and they run to get the nearest guard immediately if they see you with a weapon. This is mitigated somewhat by the fact that without a weapon, they don't even notice you exist. Unfortunately, this is a sniping mission, so you have to carry a rifle from either the start of the level or your contact elsewhere to the nest. AND you're liable to get noticed while you're waiting in the nest for the motorcade to pass by, AND it's quite possible to go through all of this and then miss the shot anyway. This is especially annoying if you're trying for Silent Assassin rating.
Building 2 in Metal Gear was a pretty creative, if difficult, level in itself, with various types of gameplay depending on what floor you're in (straight-up stealth, running away from pursuers, shooting, a maze, and so on), but was ruined by one piece of bad level design which makes the whole thing like pulling teeth. This is that one of the elevators will only go up, and the other elevator will only go down. It doesn't help that the radio gets jammed, so you can't even send or receive calls until getting antenna.
There's a lot of hate for the passageway between the Zanzibar Building and the Tower Building in Metal Gear 2. First of all, the obstacles range from boring, to annoying, to boring and annoying. It doesn't help that the boss in the area is the Running Man, who is also really boring - you don't even get to shoot him, and you beat him by running in a circle quickly enough to lay mines before your O2 meter runs out.
The very insanely, long stairway in the communications tower of Metal Gear Solid. You CAN'T avoid getting spotted by a security camera, even when the "Throw a chaff grenade before entering new doors" worked before, forcing Snake to run up an insanely long flight of stairs, being chased by a shitload of enemies—in a game where it's usually suicide to take on more then three or four enemies at a time. Oh yes, there's also the Guide Dang It that if you ran out of the room with the camera instead of rushing for the stairs, you're stuck in an infinitely respawning chamber with no way out (it's probably a glitch, but unwinnable until you reload). Even after mowing all the enemies down, the towers are still irritating for the insanely long time it takes to go up and down it, even when Snake's running.
Made even worse in the Twin Snakes Gamecube remake of the game. Try making a "no kill" run while being chased up the stairs by an endless swarm of mooks. At least it averts Cutscene Incompetence by forcing you to go through an unavoidable laser detector instead of using chaff-proof cameras.
In Metal Gear Solid 2, the part when Raiden gets his clothes taken away and has to sneak through Arsenal Gear while avoiding Arsenal Tengu (who are ten times more alert and dangerous than the Gurlukovich mercs) is That One Level.
Metal Gear Solid 4 has an Eastern European level that focuses on the player tailing a resistance member. Instead of a normal sneaking mission, it plays like an Escort Mission where the escortee will run away and spend a good while hiding if he sees the player but will gladly approach any PMCs just to make sure the player stays busy. The resistance member tends to take a strange route in any case, and will resort to backtracking or running in circles if disturbed by anything. The entire process is going to take a while.
Averted if you use one of the B&B Corps' or Raiden's masks with the civilian outfit. The resistance members won't regard Snake as hostile, which makes the mission loads easier since you only have the PMCs to worry about.
While the aforementioned escort segment is frustrating, on The Boss Extreme it pales in comparison to the bike chase that follows it—especially when going for a no-kill Big Boss Emblem run. It requires an absurd combination of precision, memorization, timing, and luck.
Thief had "The Haunted Cathedral". You're exploring ruins of an abandoned section of town filled with irritating undead, and any valuables worth stealing are very well hidden and difficult to find. You're likely to finish the main objectives within twenty minutes, and then spend the next hour or two searching every nook and cranny of the quite large level for enough loot to trigger the end, while constantly having to deal with zombies (which are not nearly as fun to work around as human guards). In general, any level in which you're dodging undead tends to be annoying, but at least loot is generally easier to find in them.
ObsCure: The Aftermath sort of does this with Mei's sister, Jun. It's almost painful enough to just let her die before she goes into it.
In Resident Evil: Code: Veronica, there is a sequence where you're forced to run away from a giant mutant zombie chasing you down a hallway while swinging a giant axe. It's extremely difficult to avoid getting hit, and if you're low on herbs/first aid sprays, it's practically impossible to pass this part since one hit knocks your health from "Fine" to "Danger", and you move slower as you get hurt. Restarting the game is painful as well since this sequence happens late in the game.
There's also the first fight against Jack Krauser, which is one big Quick Time Event that results in instant death should you press the wrong button at the wrong second. Although you frequently deal with these throughout the game, this fight strings so many of them together that the result is an arduous Unexpected Gameplay Change. The fact that the buttons are randomly generated each time doesn't help much. However, this is probably a case of That One Boss since the spiked difficulty doesn't carry over to the level itself.
Resident Evil 5, from the ending of chapter 5 onwards, changes from "Majini" to "Majini with assault rifles". Which is especially horrible since you can't run with a gun but the enemy can. Good luck.
There's lots of difficult parts in this game that can cause you to get stuck for an hour or two. One part that stands out is a section near the end of the game, where you have to fight two Reapers that attack at the same time. They both have instakill attacks and require you to aim at specific body parts to kill them. And a few moments after the giant insects appear, two Gatling Majini (who have massive hitpoints) and a huge amount of melee Majini come to attack you, and it's mandatory to kill the two Gatling Majini. Better kill the Reapers quickly or you'll have to face all of them at the same time.
Earlier in the game, you are required to navigate through underground tunnels, and if playing single player and you don't know you can have the AI partner carry the lantern, you get stuck with it instead. You will find enemies in these tunnels and you will need the lantern to see them, but to kill them, you need to put down that lantern to use your weapon.
Resident Evil 6 is similar to 5, mentioned above, in that you not only see zombies, but also gun-wielding enemies, without being able to run and shoot. The highly irritating J'avo form the main enemies of two campaigns, and most of Ada's campaign — plus, they have Adaptive Ability to make them even more of a threat.
The second mission in Jake's campaign. First, you have to find three data chips in a snowstorm where, guess what? The visibility will frequently drop out due to the swirling snow. Some of the enemies faced include very stealthy flying enemies, who don't need the snowstorm to hide from you before attacking. This gives way to a retread of the siege from 4 that then triggers a tricky downhill snowbike race ahead of an avalanche. And then there's the Paranoia Fuel chapter, where you have to wend your way through caves filled with tracker-bugs that will summon the Ustanak for an instant game over if they spot you...
The Thing has a stage almost identical to Metal Gear Solid's staircase sequence, except you're going down, there are automatic turrets on every level (that can take up to five grenade hits to destroy), scalding steam vents, seemingly endless streams of scuttling creatures that pop out of dead bodies (and attack you from front and behind), and the medic, your only hope of surviving the stage, turns into a monster at random points. If you don't have enough health packs on you, or enough firepower, it's impossible to get through the stage.
The infamous Water Part from Amnesia: The Dark Descent. Mostly because it's the first area of the game where something is relentlessly pursuing you and where you could most likely die your first time. Other than that, it involves platforming on boxes to prevent the monster from chasing you, using a lever that will open a gate for a limited time that you have to rush through. And a made dash through multiple flooded hallways, shutting door behind you to stall the monster for a few seconds.
Also the prison has annoyed some people due to it being full of intersecting dark hallways where a Servant can ambush you. Also there are multiple Servants in this area.
For first time players who made it past the first two Suitors, Amnesia: Justine has the Dungeon, and it will mostly likely be the place in which they die. Remember how easy it was to sneak around before due to the Suitors being blind? Guess what? The area is completely water-logged, so good luck trying to be quiet! The game forces you to move quickly as well due to the timing required, and there's literally no room for error, especially if the player wants to save the hostage. What makes it even worse is that the game's official ending is literally minutes away at that stage and that dying will mean starting over since there's no saving the game.
Zombies Ate My Neighbors: Has several, but the water levels (Look Who's Coming To Dinner, Creatures Of The Blue Lagoon, etc,) after level 18 is when The Fishmen start getting fast, able to catch Zeke/Julie easily when they swim, and NO, you can't use weapons while swimming. Oh, and The Fishmen can kill The Pool Guy, with ease.
Dead Space: Chapters 3 and 4 both have stages where you will wish you could just be throwing down with a swarm of Leapers. In 3, there's the gravity centrifuge, which when engaged means you need to run through it - and if you're out of a niche when the blade comes along you're reduced to a red smear on the ground. In 4, at one point, there's an objective where you need to run from cover to cover in hard vacuum and zero-gravity to avoid an inconvenient meteor shower. The hint you get for this is vague and unhelpful - it talks about "the walls" but it's not actually the walls that save you - and being caught out in the open means you get a warning about meteor impacts about, ooh, one second before you get torn apart by one.
The level in every other Star Wars game that forces you to play the "Snowspeeder wrapping up the legs of the AT-AT" level.
Notable Features of this Level: You must defeat all AT-AT's to complete the level. You must use the speeder on this stage (and/or AT-AT's can ONLY be defeated by snowspeeders). You cannot just shoot them. There are lots of other enemies you can accidentally run into (and die from) while looping. A time limit of some type, while not mandatory, is encouraged.
Various examples: Rogue Squadron 1 through 3 (N64/GC/PC), it depends on the exact game/level, but it hits practically ALL of the above.
Rogue Squadron 1 took the cake with it's Corellia Mission. You only had to take down one AT-AT, but it was at night, with the target walking along a cliff face, leaving you with a much reduced safe lane on one side. And since the mission is dark, it's hard to see the cliff. Have fun.
The Empire Strikes Back (NES/Gameboy), while the speeder part wasn't too bad, if you crashed you had to continue very slowly on foot.
Shadows of the Empire (N64), you 'can' shoot them to death in this one, but it took forever.
Lego Star Wars II (various), in Freeplay mode you could fly a different craft, but the only one that could defeat an AT-AT was the speeder. One of the less annoying examples the looping was fairly quick and easy to control (the infinite lives nature of the Lego-(something) games also helps).
The Battlefront games are at least nice enough to let you kill AT-ATs with sustained rocket/turret fire, as opposed to the speeder trick, but it also opens the door for Genre Savvy human players on the Empire's side to drive the AT-AT and knock out the turrets before Rebel players can use them. And may the Force help you if the Empire decides to rush in and capture the Echo Base hangar right away, depriving you of snowspeeders.
Star Wars Trilogy Arcade's Battle of Hoth stage skips the cables and has you shooting the AT-ATs' heads off by the neck.
Adding Fridge Logic is the fact that the Rebels have canonically taken out AT-ATs without cables, Insert Grenade Here, or rammingnote Hobbie Klivian did this in the novelization of The Empire Strikes Back. In Isard's Revenge four of the Rogues take out four walkers in about five minutes. Of course the difference is, that time they were using dedicated combat vehicles (X-Wings) instead of glorified pickup trucks with popguns. And it's not just the EU: in the actual movie, after tripping the one walker a snowspeeder finishes it off with a laser shot to the joint between the neck and the body.
Play a Star Wars space simulator. You will hate the Gallofree Yards Medium Transport. And to think, the Battle of Hoth had that just after the AT-ATs.
Star Wars Rogue Leader has the Razor Rendezvous level, where you have to take down an entire Star Destroyer by yourself. With dozens of very accurate laser cannons ripping you to shreds the whole time.
Razor Rendezvous is usurped by the game's other That One Level: the Battle of Endor. In this level you have to destroy two Star Destroyers at the same time... with a strict and very short time limit!
Both aren't nearly as bad as the final Story mission: Strike at the Core. You have to protect Lando (or Wedge, if you're playing as the Millennium Falcon) from being shot down by TIE Fighters, and it is no exaggeration that you can get an instant Game Over in under ten seconds.
Pharaoh has Thinis, the seventeenth mission. Up until then, things have been slowly building up in difficulty, but then the Old Kingdom crumbles into civil war and you face what is probably the hardest mission of the game: ressources are scarce, spread all over the map, your objectives are upped from the last mission, and you have to defend a small complex in the mountains. Seems pretty easy, except the two fighting dynasties will try to bribe you, and you must choose well. Large Nubians raids happen every few years, as well as huge good requests from pharaoh himself. You must defend from attacks from the north, from the south, and from the river, while also building your city, preserving your rapidly declining reputation (through hard-scripted events), trying to keep your budget positive at least at the end of the year, so that debts don't influence your Kingdom Rating. At some point, Pharaoh asks for military support in a city, and you have to send quite a number of troops to succeed. You're also attacked precisely at the same time, so you must have a large backup force, and a navy is necessary. Finally, if you don't support pharaoh, a trade route closes, which is your only access to a specific resource needed to complete the objective, making the mission unwinable.
Yes, an example in a visual novel. Specifically, the beginning of Hate Plus Day 3 on *Hyun-ae's route requires you to make a cake, whether it be a proper cake cooked in an oven for tens of minutes, or a cheap 5-minute cake like she offers. And we don't mean a cake in-game, we mean a real-life cake. For those who have the ingredients and equipment on hand, or cook things regularly, this shouldn't be a problem. For those that don't, this becomes a problem because your only other options are to either fake it, causing you to wait around, or admit to not making a cake, which *Hyun-ae will chew you out on. You can Take a Third Option and buy a cake instead of making it, but you don't get to explain this to *Hyun-ae until enough time passes that *Hyun-ae thinks you've been making a cake.