Crash Bandicoot 3, the motorbike levels.
Sly 2, the Indian water-bug mission
Resistance FoM, Cheddar Gorge.

The Imprisoned battles and Silent Realm trials in Skyward Sword. I don't like things that technically feel like they are timed. I prefer to be able to go at my own pace with things, not feel pressure while gaming. Life has enough of that.

I used to really hate the Palace of Twilight in Twilight Princess because of the two hands chasing you while carrying the Sol? (light) orbs. Again, pressure. I also DESPISED the damn bird/kargorok that would drop the bomb while you're trying to lead the wagon safely to Kakariko through Hyrule Field. Until I realized what was happening, I went around in a circle for 20 minutes putting out fires and fighting off never-ending Bokoblins. Frustrating.

I'm sure there are a bunch of specific platforming levels that have driven me crazy over the years (DKC and Mario), but I can't think of any off the top of my head at the moment.

A lot of my least favorite levels have already been mentioned, but here are a couple more. The ship graveyard in uncharted 3 was pretty bad. I also hated the final section of the last of us. I also hate any locations in rpgs that take place in a mine.

The Catacombs - Dark Souls

I would say it's better than Atlantica in Kingdom Hearts I

And also, in terms of mini game levels, KH has some awful ones. I'm currently playing BBS HD, but I've run away temporarily to avoid having to play with ice creams, do the command board or rumble racing

EDIT: NOT TO MENTION THE STUPID GUMMI SHIP LEVELS

The flying levels on Crash Bandicoot 3 ugh

I think this one's been echoed enough times, but...

pretty much any water level that requires some sort of breath holding gauge.

#2 for Most Hated Levels would probably include any escort mission/level in a game that wasn't specifically built around said design mechanics.

The cutscenes in Metroid Other M.

Forest temple in OoT. I find that one more tedious than the rest of the dungeons in the game honestly. It had the most punishing backtracking system...

The Imprisoned in Skyward Sword can go fornicate itself with a cactus.