I don't like the queues for some of the old Fantasyland rides - particularly Peter Pan. They are too narrow and everyone is squished in like sardines. Especially bad when it's hot out and you're sweaty.
The other one that bothered me on our last trip was Roger Rabbit. I can imagine it being fine if there is a long line, but we were among the first ones in Toontown one morning, so we went from brilliant sunshine into the dark, twisty-turny queue (and went all the way through without stopping) and I was pretty sure I was going to throw up by the time I got to the front.
I like the queues like TSMM the most b/c they are able to close off part of the area when the line isn't so long. I hate going through the whole maze at full speed.