If anyone's still reading this thread, here are some of my pet potential fixes and personal SE candidates (from memory-- DE framecounts to follow, if I get a chance):
Most are category 4, by the way.
Jumpcut of Artoo on the Blockade Runner right after he drops his third leg and rolls towards 3PO
Same shot: Artoo clearly about to roll right into a bulkhead
I've never liked Vader's first closeup-- his mask is flatly lit, with no specular highlights. Perhaps this could be improved with a selective exposure tweak.
Escape pod, "Are you sure this thing is safe?": Porthole on the inside, but not on the outside! I suppose we could retcon that it's a viewscreen instead of a window, but it would be the only circular one in the film...
Lars homestead: Red droid is still sitting to Artoo's left, after it has rolled ahead and exploded. I have an idea for how to fix the continuity here by altering the shots of Luke and 3PO so that the jawas collect Red (and presumably roll him back to where he was) before 3PO points out Artoo to Luke.
Luke's garage: In the SEs, the beam from Artoo's holoprojector is missing from a couple of shots.
Also: Full-sized stage technician disguised as a jawa, hiding behind the dandelion droid while Artoo rolls towards camera. I never noticed this until the DVD blooper reel, but it's actually in the finished film!
Tusken carjackers: How I wish those rocks weren't so obviously placed to hide the supports on the landspeeder...
Ben's hovel: Jumpcut on Luke's lightsaber ignition. Roto animation on Luke's lightsaber disappears for one frame.
Death Star conference chamber: The chrome casters on those office chairs just bug me.
Leia's cell: Crash-zoom on the Torture droid's needle is stylistically at odds with the camerawork in the rest of the film. It always reminds me I'm watching a movie from 1977.
Mos Eisley: wretched roto "floating" effect on the landspeeder as it drives past the camera. The SEs took a shot at fixing this but the new shadow makes it look like the speeder is hovering way too high off the ground. In fact, the core problem is the composition of the shot: to sell the 'hovering' effect Lucas wants us to see daylight under the hull, but the position of the sun would place the shadow behind the speeder! Check out the shot-- all the other shadows are facing away from the camera, not towards it! Somebody out there with serious 3D experience want to take a crack at generating an authentically-positioned shadow, just to see what it would look like?
Docking Bay 94: "What a piece of junk!" There's no radar dish (or gun turret) on top of the full-size Falcon mockup...
Lightsaber training: More jumpcuts on ignition and shutdown. Blade looks more white than blue, and is much thinner and sharper than when we saw it in Ben's hovel. I'm not 100% sure whether saber-animation overlays were applied to this scene or not-- this sequence was definitely treated differently than the other lightsaber scenes.
Coming out of Hyperspace: The Falcon's engine flare element is out-of-sync in the composite, and precedes the ship itself by five frames, revealing the unilluminated rear of the model.
Death Star Docking Bay: Silhouette of the Falcon model's support pylon is visible within the door's lighting effect.
Control Room: Jumpcuts on the sliding door. Jumpcut on Artoo dropping the third leg again.
Conference chamber II: On "I must face him alone," I think. Vader makes a hand gesture completely unconnected to the dialogue being spoken.
Ben skulking in the corridors, on his way to the tractor-beam junction: Why does he keep taking his saber out? These are obviously alternate takes of his approach to Vader, and one is obviously flopped left-to-right. I would at least like to remove the distinctive R2 unit in the background of that shot.
Lightbridge: Jumpcuts on the door. Also, the echo effect on "wrong turn..." varies drastically from mix to mix.
The duel: Jumpcut on Ben's saber ignition. Not as distracting as the others.
Also: I swear there's a moment where Ben and Vader's swords switch colors on impact.
The duel, continued: the notorious shot where Ben's saber isn't illuminated properly. It still looks like crap on the official DVD-- they just added a glow to it.
Ben gives it up: There's got to be a way to make that step-framed slo-mo shot play smoother. Morphing between frames maybe?
"NO!": Everyone's favorite-- Vader's saber goes white as he walks toward the blast door...
"I'm melting!" Reaction shot of Artoo looks like it was shot in the Control Room set.
Yavin approach: The Falcon really ought to cast a shadow on the trees beneath it.
Death Star Battle: That one shot of an X-Wing where the anti-aircraft fire in the background looks like dabs of Liquid Paper. Also that one shot where a T.I.E and an X-Wing seem to be floating in limbo 'cause the background isn't moving correctly.
One of the last shots of Tarkin has a weird wobble in the background. It looks like they lifted the shot from an earlier scene and had to split-screen Vader out.
Vader escapes: Vader's ship somehow passes under a shadow in the middle of outer space. Perhaps a nearby Star Destroyer?
That's off the top of my head. Anyone?