I Am Legend: a home video version with an entirely different ending, in order to open the door to a sequel.
http://www.movie-censorship.com/report.php?ID=4949
Not a visual alteration: Disney substituted the opening song lyrics on all home video versions and theatrical re-releases of Aladdin after complaints during the original theatrical run.
http://articles.latimes.com/1993-07-10/entertainment/ca-11747_1_altered-lyric
(I learned about this one from a documentary, turns out that Disney had already prepared alternate song lyrics in the event of complaints.)