Batman Begins - With Danny Elfman music. Having a REAL musical score would enhance this film so much. Batman and Batman Returns would be the two greatest sources obviously, but other Elfman scores such as Edward Scissorhands and Sleepy Hollow could be utilized as well.
Superman III - Re-sequenced and re-edited to downplay the more ridiculous aspects and focus on Clark/Lana, and Evil Superman. The junkyard battle would be the climax of the film. Perhaps have the supercomputer (Brainiac by any other name) be somehow responsible for Superman's disturbing behavior change.
Superman III/IV - A combination of Superman III and IV. I have no definite ideas for this, but I think it would be interesting to try and make something out of these two ultimately dissapointing films. I do have some vague ideas though: The Smallville part on the farm in IV can tie into the Smallville stuff in III, Nuclear Man being the cause of Evil Superman, and possibly using the Voice of Jor-El instead of Lara.
The Batman Begins edit could start at anytime, but any attempt at Superman should wait until the 14 DVD set is released later this year.