Boba Fett's voice
Anakin ghost/ eye color/ eyebrows
a couple of minor edits to the ending celebration
(someone else pointed out) the Krayt dragon or whatever call was changed into noise of the thingie Obi rode in Sith
Now, don't say the emperor, because that change should have been made A LONG TIME ago. You know, way back in 1997. I know the dialouge is negligable, but the monkey lady.. no way. I mean it was either this or change Ian in RotJ into the monkey lady. It never should have been two different people, even before the prequels were made.
I challenge someone to find things that were changed besides the four (maybe five) I posted above that were changed because of the prequels. Everything else was changed simply to improve the effects/ original vision, but not because of the prequels. I mean most of the changes were made in 1997 two years before Phantom Menace!