The Simpsons Movie (alternate versions and deleted scenes)
The Simpsons Movie went through many revisions, even while the film was being animated.
Much of the official DVD's commentary is dedicated to talking about all the different versions of the movie that exist. For example, in one version, Lisa's love interest is Milhouse, and in another, Marge is the one who's spoken to by God, and not Grandpa. (This is where the "here's the money shot" bit in the trailer comes from.)
Many of the changes were hinted at in the marketing. The tie-in toys at Burger King were supposed to have lines from the movie, but all of the lines were cut out by the time the movie was released. There is also a TV Guide article detailing some of the cut scenes. Supposedly, there exists an hour and a half of fully animated cut content, and another hour and a half of content that didn't make it past the animatic stage. This means there's three hours of deleted content, or enough for another two movies.The film is approaching its tenth anniversary, and as of right now, just under five minutes of cut content is available on the DVD.