For me, I know of a few major ones.
1) The Illidari Council in BT gets healed faster than you can DPS them down, ever. We believe it's due to SMITE, since our guild Priest's smite seems to heal anyone around who gets nailed with it.
2) Malygos's phase 2 (Drake phase) starts him back at full life, which makes things impossible to beat.
3) Any of the wyrmrest raids are difficult to get back into without being DC'd when you wipe. The gryphons getting back down to the bottom of the tower cause 2 disconnects, one when you get into the tower with it, and one when you reach the portal. The second sometimes does not happen, but the first always does.
4) Ulduar's Yogg-Saron is impossible to kill.
Again these are just the ones I've experienced. It's really hard to do much of anything right now other than ICC. My group got to Syndregosa the first 2 nights, but when we went to Ruby Sanctum, we couldn't down one of the mini-bosses. He debuffed 5 players instantly and just wrecked our tanks before anybody can do anything, and that's not a strategy issue, but I don't know that it's an actual bug like the others I've listed.
If you have some not listed here, post what you have. Hopefully this will get looked at, and possibly some hot fixes going through. It would be grand to be able to run things other than ICC or Naxx, but it's very difficult to do.