A couple of nominations from me:
G-Force (Drayton Manor). Luckily I didn't have to wait in it, since the day I went to DM we were probably 2 of about 200 people in the park. It's hideous though, and made even worse by the awful radio station playing really loud crap music.
All the Disney dark rides like Pinocchio or Peter Pan which are just endless switchbacks in front of the loading platform. The thing is, these would be fine if the queues for these rides were as short as they should be, but because Disney doesn't seem concerned with quantity of attractions or capacity, they end up being torturous affairs full of bored kids, shuffling back and forth, and the knowledge that you're waiting all this time for a minute long dark ride.
Colossus - I know the longer queue is good, but I just have memories of visiting all the time around 2002-2004 and waiting for hours in that bloody run up to the station, under a rusting lift hill and surrounded by graffiti, gum and annoying teenagers (which I wasn't, of course!)
RC Racer (WDS) - you end up walking straight through the good bit and waiting in a shed of switchbacks with French people cutting ahead. This queue also makes me angry because there's absolutely no reason why Disney doesn't have 2 or 3 of these rides lined up next to each other to increase capacity - they're relatively cheap, it wouldn't really ruin it aesthetically (I guess you might have to explain to some kids why there are two RCs). It's typical Disney laziness which shouldn't exist. On a similar note, Crush's Coaster, which I've never queued for because, much as I'm sure it is a great ride, whoever thought it was a good idea to put a Maurer Sohne spinner into a Disney park obviously didn't understand the theme park industry very well.
And some good'uns:
Oblivion (Alton Towers) - I'm actually almost sorry that I've never had to queue all the way through it, because the way it keeps looping under the station, with the videos and progression of tension is very clever. Also a cool view over X_Sector. Ruined by the fact that you seem to get stuck in those cages at the end for hours, and because it is way too wide and therefore has potential for queue jumping (or Fastpass as I believe it's now called!).
Kilimanjaro Safaris - It's Animal Kingdom, so it's obviously lush and beautiful and well themed. I'm sure Everest is just as good, haven't been since it opened.
Men in Black: Alien Attack - it seemed to me as though the queuing area was about the size of another ride!