There are binary file comparison programs out there, but I didn't want to clutter up my HD with even more stuff. So I did a quick search for an online comparison site. I found this one:
http://www.diffnow.comIt's a little slow because it displays the entire contents of both files. But it is sooo useful! Want to know where palette data is stored in a game but only have a game editor like reVamp or Stake? Backup the game, edit a palette entry, save it, then load both copies of the game into that site. Click COMPARE and voila! It tells you all the bytes that got changed!
Man, this will make my weekends go by so much faster now.

On a sad note, this verified what I'd discovered on my own: you can't have multiple background colors in CV3 (not sure about other NES games) because Trevor's transparent color is the background color. Although sinc eyou can have more than one background color by directly editing the PPU, I would think it was just a limitation Konami put on themselves.