I did a bit of experimenting with the AviSynth filter ColourLike: http://forum.doom9.org/showthread.php?t=96308
Works by generating histograms from one source and modifying another to more closely resemble it. Tried it on the rancor scene in RotJ, modifying the 2004 version based on the GOUT colours (with a saturation increase and hue shift away from red) and the results seem promising.
I have a feeling it probably works better when the sources aren't too radically different--the scenes of Luke lost in the snow in ESB looked pretty terrible; the colour was mostly right but some elements became inexplicably bright purple(?!) and there was crazy blocking going on in the backgrounds sometimes. That whole sequence is so screwed up in the SE, it's like there's a thick blue haze over the entire image; so manual correction is the only way to fix that, but it works better elsewhere. I don't remember if this is the same method that was being discussed a couple years back or not.
Of course this filter can only work with the data that is already present in the SE images. Parts that are completely desaturated, like the Star Destroyer laser blasts in the beginning of ANH, can't be rescued with such a method.
I put up a few images for comparison. I'd be curious for any opinions. Right now I'm just experimenting with this, but I might continue if it works well enough. As I've said, I'm not really wired towards video the way I am with sound, but it's interesting in its own way.
Jabba GOUT: http://img689.imageshack.us/img689/6792/gout2.png
Jabba SE: http://img228.imageshack.us/img228/4076/se2h.png
Jabba test: http://img683.imageshack.us/img683/9264/test2o.png
3PO GOUT: http://img59.imageshack.us/img59/4723/gout3.png
3PO SE: http://img696.imageshack.us/img696/3185/se3.png
3PO test: http://img69.imageshack.us/img69/4089/test3c.png
Luke GOUT: http://img15.imageshack.us/img15/1589/gout1.png
Luke SE: http://img96.imageshack.us/img96/1327/se1v.png
Luke test: http://img703.imageshack.us/img703/706/test1zf.png