I'll update this list as I think of more.
Oblivion: Oblivion Gates: Not that they were bad, they were very well designed. They were however very repetitive after a while.
Halo Combat Evolved: The Library: All of the mystery, wonder and scenery of Halo replaced for an hour by repetitive corridors and just mindless waves of enemies.
Dragon Age Origins: The Fade: While again not 'bad', I always skip this section with the 'Skip the Fade' mod simply because it doesnt change on subsequent playthroughts, gives no options in interaction or decision making, and is basically incredibly linear.
The Legend of Zelda Majora's Mask: Great Bay Temple: Most people cry at the Water Temple from Oot, but the Great Bay Temple is like it's demented cousin. It's not a bad temple, it's actually incredible to look at any brilliantly designed mostly, but is very tedious to work through as theres a lot of repetitive actions like changing water direction, and multiple instances where falling off a platform requires 20 minutes of manipulating water to get back to where you originally were.
Bioshock: Proving Grounds: Protecting the Little Sister is just one long escort quest. No exploration, nothing of note, just the same actions over and over. Escort sister, kill enemies, direct to retrieve ADAM, kill enemies, rinse and repeat too many times. Why they chose the worst bloody part of the game as the basis for Bioshock 2 is beyond me.
Dark Souls: Anor Londo: I just got past this section of Dark Souls and screw EVERYTHING about it. Sure it looks amazing, but suddenly having platforming in the middle felt incredibly jarring, and one section in particular (all I'll say is "Archers") isn't challenging in any way, it's just cheap and frustrating for the sake of being cheap and frustrating.
Neverwinter Nights 2: Gem Mines: While not particularly difficult, the ghost lights puzzle in this area is just plain annoying. It's slow, tedious, and if you make a single mistake you'll be swearing at yourself for the 60seconds or so it can take to get you back to where you were. Its an overly simple but slow puzzle that you need to complete about five times longer than it takes to stop being interesting.
Mass Effect 2: Mineral Scanning: Not actually a 'level', but it all takes place on the same screen so bugger it. Mass Effect felt large because you could explore planets on the ground. Sure, they were fairly empty and the vehicle handled like a drunk Irishman, but it at least gave the world a sense of scale. In ME2, we instead got a little wavey line that moved when you were over minerals, and the damn thing was so slow the scanner upgrade was necessary simply so you didnt have to spend 90% of your playthrough finding minerals.
Batman Arkham City: Iceberg Lounge; AC was all about being Batman, using his gadgets to outwit enemies and get to your goal. Then suddenly, boom, you're on an ice raft bringing the action to a halt. Not only is the bloody thing slow and repetitive to move, but it becomes a glorified escort quest. Easily the least fun part of the game.
Batman Arkham Origins: Sewers: They spend the entire time building up the tension for the confrontation with Killer Croc in the sewers, and instead its an overly long and simple fight with no challenge. Croc jumps up, hit with Batarang, run away, rinse and repeat.
Crysis: Ascension: Incredibly out of place, forcing you to pilot a VTOL that handles like an overweight drunk Irishman this time around. Worst part is, you're constantly expected to stop and enter dogfights in the bloody thing.
Assassin's Creed: The last part of the game: Actually a bunch of levels, but the last section of the original AC removes any stealth or or "Assassiny" bits and just turns into constant waves of enemies. Considering how sub-par the combat was in that game most of the time it didnt really live up to expectations.
Half Life: Xen: Do I really need to say it? Horrible, awkward platforming that broke the excitment and action and replaced it with a lot of quicksaving.
Super Mario Sunshine: The Watermelon Festival: Bloody hell, this was an escort quest-like level designed by Satan. So much as look at the watermelon funny and it explodes and you have to do the whole bloody thing again.