The Haunted mansion is my favorite dark ride. I like the queue and facade at Disneyland, as well as the hallway right before you board, again from Disneyland. However, I like the Magic Kingdom version more once you actually sit down in a doom buggy.
My second favorite would have to be Pirates of the Caribbean, as it is in Disneyland. After that, the Tower of Terror, as it is in Hollywood Studios.
What can I say? I'm a sucker for details. (and that great smell inside Pirates)