Seafoam Islands for me. That area is just frustration incarnate for me. Even when I played FireRed and had a guide to help me, it was just a pain to play through.
Zero Isle, all of them in Mystery Dungeon. I can't get past any of them. What's the point in reducing a PKMN to level one in the first place!
Most definitely Rock Tunnel (for reasons mentioned previously in this thread) or 70% of water routes. I -hate- Tentacool/Tentacruel/Wingull/Pelipper sooooo much because of these. I also get very annoyed by caves because, unless I have a ton of Repels, I'm pestered by wild Pokemon every 5-10 steps.