As you can see in the announcement below, the disc version of the film will feature an “extended version” an an “alternate ending.” We would like to comment further on this, but we haven’t seen the film yet. So we have no idea what could be different. Yet.
There is much speculation that there could be more Hulk in the end. In the normal version he seems to just disappear with only a quick explanation by Nick Fury that apparently left many fans unsatisfied. Other rumors suggest an additional post credits scene. Though I certainly dont think that the extended cut will be the original 3 hours cut that Whedon had.