I noticed in the OOT that Vader's helmet in the "I am your father" scene wobbles a bit. I think that it could be stabilized. The SE might use different shots for these lines where it wobbles in the OOT, but I am not sure.
In the run between docking platforms on Cloud City, it can be seen in one shot that Leia carries a different revision of the stormtrooper blaster than in other shots - it has two greeblies on the scope rail that aren't present on the props(s) she is carrying in the other shots.
Edit: It is the shot when R2 tries to interface with a terminal but gets a jolt of electricity instead. Leia is holding the blaster stationary by her side, and there is only a white wall in the background. The shot is also very short, so all in all I think it that the extra greeblies can be painted over easily.
Oh.. And don't forget the goof in the ESB-SE with the stained-glass windows when Han, Leia and Chewie meet Vader. Replace the windows behind the stormtroopers with cityscape or reuse OT footage in the preceding shots (easier).
ROTJ
Of course, I absolutely hate the revisions made in the SE, and very much prefer a very alien Lapti Nek, Ewok Celebration and a ghosty Sebastian Shaw over the later revisions.
Personally, I dislike the droid torture and would like this shortened. I know people who absolutely love this scene and have Eve-9D9 as their favourite character ... so I am aware that a lot of people disagree with me. At least remove the cartoonish screams.
If possible, Jabba's lips could maybe be a little more articulated.
I think it would be great if Bib Fortuna's tentacles would move a little. Maybe tighten or loosen around his neck, or the tip of a tentacle wiggle a little. I think it would be most fitting when he is in the background.
In ESB, when Han Solo is lowered into the freezing chamber, he is wearing restraints around his arms, tied behind his back. These are not there when he falls out of the carbonite block!
They should either be removed in ESB or added in ROTJ. I think it would be easiest to remove them in ESB, but it would be better if it could be pulled off with them being there in ROTJ, just because they look cool ...
At least four different props were used as Luke's lightsaber in ROTJ. I think the most apparent difference is that the saber that is shot out of R2-D2 does not have the knob at the top of the emitter, which the other ones have. Could this be added?
Should Leia be present at Vader's funeral pyre? I am not sure of this myself, though. What do you think?