Haunted Mansion Holiday was supposed to come to Magic Kingdom too but they decided that they didn't want holiday overlays taking the place of the actual attraction just because of how many tourists come to WDW. All of the props that were made for it are currently used in the Tokyo version.
Also this is something a lot of people probably know about, back when the haunted mansion first opened there was something there that no longer is in the ride, the hatbox ghost, the effect didn't work as well as they planned so they took him out. It's been rumored that he's going to return soon. He made an appearance at D23 last year too!
http://www.youtube.com/watch?v=cLFD-TBRdgA
Discovery Island & River Country are 2 abandoned places at WDW. Both left to rot, with lights and music always playing even tho no one's there.
http://www.youtube.com/watch?v=Q4JwgmPEIDQ
The Wonders of Life Pavilion still has cranium command intact even though the original Pavilion has been closed since 2007. The Body Wars Queue is also intact but the simulators have been gutted.
The abandoned upstairs of Imageworks still sits there left to rot which is very sad
http://www.disboards.com/showthread.php?t=2479130
http://www.youtube.com/watch?v=jKCp6LsYKcU
Food rocks, another abandoned thing by disney is possibly still there as of 2007 it's just covered up by the soarin queue area
http://forums.wdwmagic.com/threads/food-rocks-pics-sept-24-2007.229181/
Another eerie secret is that an old max animatronic from country bear jamboree is destroyed and under the seance room in haunted mansion.
http://www.imagineeringdisney.com/blog/2010/4/24/abandoned-disney-country-bear-max.html
it's such a sad thing that a company like Disney has all of these things happening behind closed doors.