As Obi-Wan leaves Mustafar, there is a shot of him sitting in the cockpit of Padme's Naboo skiff, with C-3PO sitting next to him. The next shot is of the badly burned Anakin trying to claw his way up the lava bank with his remaining prosthetic arm. In the theatrical version, these shots were separated by a wipe. In the DVD, it is a normal cut. But in the 2011 Blu-Ray release, the wipe has been restored.
Darth Vader's drawn out "Nooooo!" after learning of Padme's death has been shortened in the DVD release compared to the cinematic version.
The 2011 Blu-Ray release has added dialogue for Commander Cody and the clones when they arrive to aid Obi-Wan on Utapau. Originally, their entrance was silent on the theatrical and DVD versions.