Lucas and cohorts have changed Boba Fett's voice in Empire (he's now voiced by Temuera Morrison, who played Jango Fett in Episode II); they've changed the timbre of Darth Vader's voice in Star Wars (it's now less echo-y and more like the Empire/Jedi voice); they've completely replaced Ben Kenobi's krayt-dragon call (the one that scares off the sandpeople) with a new sound; and worst of all, they've significantly lowered John Williams' score in the mix during the final Death Star fight in Star Wars.
Now, I have to admit that the re-voicing of Boba Fett doesn't really bother me all that much, except as a purist: he's only got something like three lines, and the new readings don't strike me as any worse (or any better) than the old ones. And while I'm not crazy about the reduced reverb on the Vader voice, I can't honestly say that it sounds bad: it just doesn't match my 27-year-old memories of the movie. But the changed dragon-call effect irritates me, and the nigh-inaudible scoring in the space battle is just infuriating.
On top of all that, a poster on the Home Theater Forum has pointed out that the surround channels on the 5.1-channel mix for Star Wars are reversed – so that instruments playing in the front-right speaker are echoed in the rear-left speaker and vice versa. This issue has been brought to Lucasfilm's attention... and they have issued a statement claiming that there are no errors in the sound-mix.
At least they fixed two of the blunders from the 1997 "Special" Edition mixes. In the "Death Star chasm" scene in Star Wars, Princess Leia's blaster no longer sounds like a .44 Magnum; and in Empire, when Luke intentionally steps off the platform in Cloud City, he no longer screams pathetically as he falls. Two steps forward... two steps back. (And now we're cha-cha'ing.)