Another 1997 SW wipe redone, when searching for R2, transition of Luke getting his gun to looking through the binoculars at the Banthas. The feathering on the wipe is less in the SE. (and weird green in the 2004)

*EDIT*
Here's something completely minor. In the GOUT look above Ben's head. There's a black ellipse sticking down. Seems to have been straightened in the 2004.

*EDIT 2*
This looks like a frame stabilization, you'll need to step through the first few frames of the 2004 and anything prior. On the DS, the commander's meeting, the first 3 frames have some flexing before they settle down. The second frame jumps right, then the third frame squooshes a tad.

This may just be a transfer thing. The GOUT wobbles in the scene. See a little wobbling in the 97SE. I'm noticing much of the wobble in the lights thru the doorway.
*EDIT 3*
Another 1997 wipe redone. Luke leaves Ben and the droids at the sandcrawler to go find out what's happened to his uncle and aunt. Notice how the 1997 wipe is a little faster, 3po gets wiped a frame early.

Also this entire shot seems to be shifted 5 frames. Look at the background dirt/grass squat 'z' on the left of frame:
minus 5 frames .................. plus 5 frames

See in the 2004 (-5) the dirt pattern right behind the engine, that shows up 5 frames later in the GOUT (+5) pic.

In this pic the landspeeder is differently centered in frame, but exists at the same point in time, start with the 2004 above the engine is a zip dirt strip, in the 1977 it's above the nose of the landspeeder.
Which then means that the exit wipe was also redone in 1997:

*EDIT 4*
for this shot (Luke, Ben 3po & R2 landspeedering to Mos Eisley), might want to mention how the top half of the background is also replaced. I think they've taken a guide line where everything above 3po's head was cut and then stretched vertically.
http://picasaweb.google.com/102542760950977079734/StarWarsSpecialEditionChangesHD?gsessionid=VIEttb8ACbc2-jJMrZ3D_Q#5514975447138093666

Look at rock outcropping just in front (and above in 77) of the speeder, looks the same except in 2004 it's twice at vertical and now right in front.
*EDIT 5*
In addition to the Wolfman to Melas change the exit wipe out from the Feltiperrn Trevagg and M'iiyoom Onith shot is 1997 new.
Intro wipe.........................exit wipe

*EDIT 6*
Another 1997 revised wipe. Cantina interior to exterior 3po and r2 hanging out. The original wipe was a little busy, so in the SE they seem to have added a third wipe to remove Chewie's back and when moved the previous wipe close to Chewie's body. This allows the landspeeder engine to show up a frame earlier.

*EDIT 7*
In addition to the nonsense with Greedo shooting first, the pre-explosion Greedo, in the 2004 the background is well much darker devoid of all the previous details. (also added some in explosion weirdness, these are for the color debate of lightsabers and laser blast cores, how they've isolated a certain spectrum of white and heavily tweaked it.)

*EDIT 8*
The wipe into the SE Jabba scene, should the 2004 be added as it's a new Jabba? Or as it was all digital at that point....

Also the Chewie shot, during the SE Jabba sequence, seems to have been shifted a few frames earlier in the 2004. (on second review, this is wrong)
The exit wipe of the SE Jabba sequence is also redone in 2004, look at the relationship of Boba's rocket pack to Obi's cloak.
