I am surprised -1 has yet to cite the LOTR trilogy extended editions as yet more examples of atrocities done by film makers to their films that nobody seems to complain about.
Another one to add to that list would be the second DVD release (the first anamorphic release packed with extras) of Monty Python and the Holy Grail which had an extended scene sliced back in. I for one was among the few who whined about that, I thought the extra scene sucked, messed up the pacing of the film, and was not part of the version of the film I was so used to watching for so many years. It was one of the reasons I did not think twice about hanging onto my original barebones nonanamorphic disc instead of picking up a copy of the new release. Interestingly, on the next rerelease of the DVD, the scene was removed from the actual feature, but left accessible through the deleted scenes menu. Guess I wasn't the only one who didn't like it.
Blade Runner would have been another one to add to this list. Notice how all these have been fixed by now? All these have received a fantastic modern transfer of the original versions. Yet we cannot manage to get Star Wars Episodes 1-3 theatrical versions on DVD (seriously, if the film isn't finished yet, don't show it in the damn movie theater, especially when you have full creative control over everything in the film and have no excuse for a director's cut), and we cannot manage to get episodes 4-6 in any quality up to the standards of this century.