I'll echo a few:
Trash after Huhuran going to Twin Emps and before C'thun...such a pain in the ass.
All of the trash leading to Kalecgos in SWP. Jesus...wandering packs...double pulls...the first couple of weeks doing Kalecgos and Brutallus progression was nightmare-ish.
Suppression room in BWL w/ the never-ending whelp spawns. Not particularly difficult, but just goddamn annoying.
First few lava packs in MC when everyone was still in blue/green gear.
The final trash pull in Magister's Terrace if you had a light CC group.
Hyjal. Nuff said.