Yes, but it's difficult to list them all. Here's a few:
They've replaced the CGI Jabba in ANH with a better one.
The Emperor in ESB has been replaced with Ian McDiarmid, and the dialog in that scene has changed slightly.
Boba Fett's voice in ESB has been replaced with that of Temura Morrison (Jango Fett in AOTC). Fett didn't have any lines in ROTJ except for "AIIEEE!!!", so they didn't bother with that.
Han and Greedo now shoot at almost exactly the same time. A rather pathetic attempt to please the "Han shot first" crowd.
Vader's eyebrows have been removed in ROTJ and his eyes are now the same color as Hayden Christensen's.
Hayden has also replaced Sebastian Shaw in the end sequence when Luke sees Anakin, Obi-Wan, and Yoda as spirits. This one pissed a lot of people off.
A few more little bits here and there.. things like adding the Jedi Temple to the background on Coruscant in ROTJ, things like that.
Not to mention the digital restoration.. the films look glorious.