My personal favorite method is to use IsBoxer to rename the window's title. You can name your toons absolutely anything, just pick the first random name, and in IsBoxer you change the title to One or Two or whatever.

For the way you describe I would choose names that begin with A for first toon, B for second, etc. That takes care of 26 toons so just Aa, Bb, etc for last four. That would make it so they don't look like they are connected, but you can tell which is which. It would be easy to create, you could google a list of baby names and just pick one from each letter.