Originally posted by: Scruffy
"transcode -y im -F png" and hand-paint the trails out of each frame with the GIMP, then pipe png2yuv ...

There is also CinePaint (previously "FilmGIMP") which can work in YUV color space directly and which could be better than regular GIMP at flipping frames back and forth. I have not tried it myself yet, though. It also seems to be in an early stage of development and be based on an earlier (but not bad) version of GIMP.
Anyway...

I am not so sure that de-ghosting could be done very well automatically. I am afraid that any automatic algorithm would only add as many artifacts as it removes.
Possibly a user-assisted deghosting tool could work well for some scenes, though. In any way, doing the research, development and test of just the algorithm could be just as much work as cleaning up these three DVDs by hand using existing tools.