Something that would be neat is an overlapping encode.
Record Happy Lee's with a hacked up version of the rom where everything but mario is pink, then encode adelikat's as normal, then layer them ontop of each other with some type of re-coloring on happy lees
Actually, that sounds super easy to do, I might install FCEU and do this my self :P
edit:
Didn't come out as good as I was hoping for. This is "adding" the difference between the two videos in: [URL=
http://red-stars.net/random/walkathon2335_and_2330.avi]walkathon2335_and_2330.avi[/URL] You get a green mario when ever happylee does not line up. It's a decent effect.
And this is the two runs them side-by-side, [URL=
http://red-stars.net/random/walkathon2335_and_2330sidebyside.avi]walkathon2335_and_2330sidebyside.avi[/URL] (happylee is on the left)
I made the hacked rom, but was having trouble getting the random solid colors to be blacked out in AviSynth. I'll give it a second go later
for the first file:
lee = AviSource("happylee unhacked.avi").Trim(64,0)
kat = AviSource("adelikat-smb-sidestroller.avi").Trim(458,0)
viddif = Overlay(kat, lee, mode="Subtract")
return Overlay(kat, viddif, mode="Add")