Lost Izalith and Blighttown in Dark Souls are two of the most annoying areas for me. They're easy to get through (I always pick up the Rusted Iron Ring for Blighttown) and while I like looking up in Blighttown since you can see the sky (and it keeps the framerate a bit smoother), the poison is a pain. But there's nothing redeeming about the lava pit in Lost Izalith. Seriously, did anyone not think to drop the contrast on that lava? It's more offensive to the eyes than neon green and neon yellow.
Still, nothing bothers me more than the Nino Ruins in Megaman Legends 2. Between the constant changing of water levels, how your speed gets cut to around 25% speed when underwater, further combined with the lowered framerate, water-simulating wavy screen-filter, and how when you get hit your falling animation lasts for-freaking-ever, just makes this an awful, awful level. Add that to the fact that if you want to make all the weapons, you'll need to be really good with jetisonning yourself off of platforms with the Hydro-skates (while underwater) to get some of the materials, and you also have to go back there later and break down a bunch of walls (alternating water levels again).
To make matters worse, you can go through this crap again in an optional dungeon...IN THE MIDDLE OF THE FRIGGIN' DESERT! I get what they were trying to do--give you that feeling of being underwater--but, ugh. It's just too tedious for me. Plus, after I'm out of those dungeons, I'm so used to everything moving so damn slowly that the game feels like it's playing in some turbo-mode once I'm out of those dungeons.