Most hated locations, dungeons, or maps in games.

The wind level in Ninja Gaiden. I had nightmares from the spider boss.

Its not really a location, map or a quest, but GTA VC RC Helicopter mission still gives me nightmares, even after all these years...

Temple of trials, Fallout 2
Wailing Caverns/Dire Maul etc, World of warcraft
Xen, Half Life

GTA: SA I HATE PLANES! God I NEVER had one successful landing. Even in so many tries during the tests... The only plane I could fly was the special fighter as it can fly like a helicopter, but the others... More or less everytime a meeting with the bottom... with no good end.
While planes are no place: Airports with normal planes! The only excuse for my bad flying could be I used a keyboard.

The spot of open ground big enough to cross, but there is an invisible wall or easily passable barrier. internalized screaming

The Great Sand Sea from The Last Remnant

Mindflayers dungeon in BG2, Kangaxx too. And vampires. I had nightmares they sucks my levels ..xDD
Mafia 1 - car race
HL2 - Ravenholm
Masquerade Bloodlines - Haunted Hotel

Lots of them, mostly because of the dungeons built like a maze and also looked almost the same as last room entered or last floor and i will stuck for hours.

I hate caves. All bloody caves. I get lost easily, all the walls look the same, there's no sunlight(duh!), if you try to look in the map it's a bloody maze(specially on fallout 3 and new vegas, don't remember about that on 4) and if you're playing pokemon they are freacking zubats infesting the zone like a plague.

Dungeons in general have maze-like maps, but caves are just the worst.

Clanker's Cavern in BK. To this day I have never hated anything as passionately. Clanker might be an alright guy, but his cavern is an eternal shit stain on the face of gaming history. It serves as a living testimony for me that no amount of aspiration and prestige will ever make a water level not be a steaming pile of fucking garbage.

I can't remember something appropriate from single-player games, usually I'm patient, besides single-player game ends sooner or later. (By the way, Minoan Labyrinth is interesting choice, although I can't say that it made me so angry). But from online games first comes to mind Firelands, a raid instance from WoW - visit this place many times for a while and constantly see this lava around and the bright red, it was quite painful for eyes.

Right offhand:

Arkham Asylum - The elevator shaft
Arkham City - The underground subway. SUCH a maze, and so easy to lose bearings!

Star Ocean 3: Test of Time (PS2) - Final "dungeon". Same thing over and over again, SO tedious! The rest of the game is awesome!
Wild Arms 3 (PS2) - Abyss (optional) dungeon. 100 levels, and you if you have to leave, you have to start over. Ugh. Good loot at the bottom, though!

Darm Tower in the first Ys game! >_<

Spinning platforms + flying medusa heads = fuck you, Castlevania Clock Tower level/segment

There's probably more, but those don't come to mind as easily as the traditional exercise in frustration.

Circus Stage in Shining Force took me a few days to beat when i really only wanted to continue the frickin game :E

+ every single level where you have to escape flowing lava, rising water, etc. you know the drill...

Panchaea in Human Revolution.

I would quote "Mire of the Damned" from MMVI when I saw the title, but I think Castle Darkmoor is a better choice :D

any part where you had to jump over some stuff or there was a part with some big hole to drop in or when climbing a plant or ladder and had to jump over to another ladder /plant and falling all the way down multiple levels or just die ;p

Double dragon comes to mind;p

Probably all Star Wars Dark Forces maps lol and as a mission i still hate that senator boss fight from metal gear rising revengeance

Any boss fight in Castlevania: Lords of Shadow that required you to rotate the "joystick" 360* I was playing on a keyboard and it was near impossible to do. I remember fighting a colossus thet required you to do thismultiple times, and if you missed one you had to start the fight from scratch....

Baldur's Gate 2 The planar sphere; first time I've got there and it moved you to other plane I was like "I want to come back:("

Generally, I find sewer (and sewer-like) levels to be really annoying in RPGs, as poison is pretty much never a fun thing to deal with. KOTOR 1 had the part with the rakghouls that fits this theme, and I really hated it. It's not hard, just annoying.

The Deep Roads in Dragon Age Origins also holds a special positions, for being overly long and tedious.

Strahd's Possession has several sections where it throws level-draining creatures at you.Tomb of the Elven Lord stands out as especially bad, as you had to fight hordes of them, but there were other areas that were almost as annoying.

The race sequence from Mafia 1. Good grief, that was annoying.

The maze from Legend of Kyranida. It's one of the most annoying mazes I've ever seen in game!