Well, I could just say “recomposited bluescreen shots” but I feel like that’s too easy. So if I had to stick to significant changes that actually change the movie and not just taking what was already there and making it look a bit cleaner…

I would say the 97 version of Jedi’s ending. Maybe it’s just because I grew up on the special editions, but I just think Victory Celebration is a much better piece of music to end it on. (Also if I were told to make one NEW change for whatever reason… I would re-redo the Anakin ghost to actually look like the Anakin we saw under the helmet. Like, seriously, why did the original have hair? Kid-me couldn’t even tell who it was supposed to be.)
Then if you wanted me to keep one per movie… for Empire I’d keep Ian McDiarmid. Sure, you could complain that the original Emperor in that scene looked more intimidating, or that 2005-Emperor still doesn’t look like 1983-Emperor, but I think I’d still like to keep the same actor who plays him in every other movie. Though I would very much like for the “Offspring of Anakin Skywalker”-line to be removed.
For ANH… Does the title “Episode IV: A New Hope” count? …Probably not. Well then the CGI spaceship shots then. I have no issue with those.