Hmm... IMO, Madokami would absolutely own Gilgamesh what with her godlike powers and whatnot.
Also, it would be amusing to see Homura beat Gilgamesh by going back in time and killing him before he became a heroic spirit- i.e. before he became immune to bullets. Just imagine it.. HomuHomu mowing down thousands of ancient Babylonian spearmen with a minigun before finally blasting her way right into the throne room!
I don't know, the Book of Darkness didn't quite have god-level powers. Perhaps Walpurgis Night would be a more even match.
Or, God Mode Madoka vs Haruhi...
Or Madoka vs Medaka... see what I did there?
BTW, I'm supporting Madoka in both matches.
Not quite an anime crossover, but, how about Oda Nobunaga (real life) vs Oda Nobuna!
I might actually do that one if I revive my
Epic Rap Battles In Anime History series.