Gojira -- rip the subtitles from the current DVD and then remake them with a new font, and fix the timing errors.
Tom and Jerry: The Movie -- Remove half (or all) of the songs and this thing might just be bearable.
My Little Pony -- Several episodes on the current DVDs (specifically, "Rescue at Midnight Castle," "Escape from Catrina," and "The Glass Princess") have missing scenes/musical numbers. Someone should re-integrate these into the episodes.
The Karate Kid trilogy -- Splice the recaps at the beginning of each to make it look like Part III takes place before Part II.
Robotech -- Make a "remastered" version that doesn't change the opening credits or commercial bumpers and doesn't have CGI logos and episode titles. Also use the original mono soundtrack.
And to reiterate the ones I mentioned earlier (since I can't find my old post or its follow-ups):
Castle of Cagliostro -- re-integrate the original animated opening credits into the "special edition" of the film.
Gundam movie trilogy -- Replace the 2.0 track on the current DVDs with the audio from the VHS releases.