#1 "Escape Plan" - This is the only quest I can think of where I would actually point to it and go, "that, sir, is a crappy design." It reminds me of Max Payne 3 where you are moving along, playing the game, and then there is a cut-scene where you screw everything up, then you are back to playing again and having to cope with the screw up cut-scene-you just made. No actual cut scene in Escape Plan, but a functional one.
#2 "Madstone Crater" - I find it long and tedious and it nullifies my favorite tactics (enchantment.) I'm not saying it is badly designed, I just do not enjoy it. Personal taste.
#3 "Against the Demon Queen" - Sadly, because it is actually an excellent quest... but I have to run it 65 bazillion times to torc farm and just getting to it annoys the snot out of me. I run it over and over on casual to flag... so it has become nothing more than a chore impeding the thing that I actually want to do (Zawabi's Revenge.) So it isn't the quest itself so much as the game dynamics surrounding it.
Honorable Mention "The Crypt of Gerard Dryden" - Amongst a series of fun short quests, this one has a bland map, vast over use of bland monsters, repeated annoying abuse mechanic, and is at a level that makes only one tactic viable. Melee. For years this was my most loathed quest.
I always find these lists interesting. CC almost always is the A#1 "winner" of this list. Personally I like CC just fine. Its difficulty/annoyances is more than made up for by the XP rewards for my tastes. I think CC's biggest issue is that it is a flagging quest for critical content. It utilizes a novelty-mechanic (which we refer to as Mario-Skills) and it is long. CC and Tomb of the Tormented probably suffer most from taking novelty mechanic and over using it.
The other one that is frequently mentioned is the Tangleroot series. Personally the same reason many people hate it is the reason I love it. The covering the same map, repeatedly going just a little bit further each time... I find that novel. Sorrowdusk does teh same thing to a lesser degree, and if this tactic was used frequently, it would tick me off, but as it is, I like it.