The special edition DVD version has never-before-seen footage of this movie and are the following:
- Lock, Shock and Barrel (the trick-or-treaters) are bored so they grab some snacks and go inside their cage/elevator to watch oogie boogie torture Santa and Sally. And later, a thought to be dead Jack Skellington enters the lair by jumping on the cage/elevator with the kids inside and he scares them which can explain how he got inside the lair at the nick of time. Pictures of the scene were in the promotional booklets, postcard books, and storybooks.
- Jack's further experiments with Christmas such as having a illustrating "Sandy Claws" as a human/lobster hybrid.
- a deleted part of oogie boogie's song that shows his shadow dancing.
- a scene where the vampires are playing hockey with the head of Tim Burton, this was corrected and Tim's head was replaced with a Jack O' Lantern.
In 2006, Industrial Light and Magic used computer technology to create a stereoscopic 3D version of the film that was released to digital 3D theaters on October 20. There are only a few differences in this version:
- The version begins with a countdown to when you should put your 3-D glasses on, which shows a jack-in-the-box that pops out revealing a Jack-o-lantern.
- The Touchstone logo has been replaced with the 2006 Disney logo, and the film now says 'Walt Disney Pictures Presents' instead of 'Touchstone Pictures Presents'
- The end credit roll features concept art from the movie that goes with the music. The credit roll itself is extended to include credits for people involved with the 3-D version of the film.
The 2008 DVD & Blu-ray releases have replaced the Touchstone Pictures logo with the Walt Disney Pictures logo. The opening titles also read "Walt Disney Pictures Presents" instead of "Touchstone Pictures Presents".
The special edition DVD also includes some scenes in storyboard form with voiceovers:
- During "Making X-mas", the Behemoth sings about the presents the creatures are making.
- A segment of Oogie Boogie's song where bugs dance from his "eyes" and end up sucked in his mouth, this wasn't animated because the dancing bugs would be difficult to animate.
- The alternate identity of Oogie Boogie where it's not a bunch of bugs but Dr. Finklestein (the mad scientist), he said he became Oogie Boogie because Sally was in love with Jack even though he created her and as Oogie Boogie he'd give her a lesson she's never forget, Finklestein then mentions a creation that will like him and with Igor's help he escapes through a trap door, this segment ends with Jack saying "i can't believe this".