Yup, I can confirm the Pirates story. I worked in merchandise at Pirates, and had friends who worked the attraction who told me all about that.
Another one is at Splash Mountain, often around drop 3 (the really little one going into the laughing place). I had a friend who worked there and swears by it. The story goes that someone was having a heart attack, and when their log stopped at the top of that little drop, they tried to climb out and when the log started moving again, they fell and were crushed. Now, they sensors there give high-water level warnings when there is not a problem. Also, one of the CMs was doing a ride-through, and when he got to hte Zip-a-Dee-Doo-Dah scene, he said there was this dark shadow movinig around the room, but absolutely nothing casting the shadow.
There's one at the Haunted Mansion, oddly enough, the "Old Man With the Cane." He is seen sometimes by CMs at load/unload, just sitting in a DoomBuggy, unresponsive.
I have heard of the one in AE, and also the Alien scene in GMR has apaprently had its share of haunts, but I don't know the details on that one.
Over here on the West Coast, Disneyland's Haunted Mansion is just rife with real ghost stories. Sooo many sightings, and Cast Members that have had things so scary happen to them that they literally ran out of the building screaming, and refused to work in there again. Sounds a bit out there... but I know someone who worked there about 14 years ago, and he insists that stuff like that DOES happen and has happened to him.
-Kirsten