Simple Rule idea:
Usable once per game during any combat. Roll all Munchkin d6 (or Rainbow d6). Add all even numbers as a bonus to the Munchkins. Add all odd numbers as a bonus to the Monsters.
This rule would give a slight advantage to the even side (since 2,4,6 > 1,3,5). To make it more Munchkinly, the evens could go to the Monsters and the odds to the Munchkins.
Or the rules could be:
Munchkin d6
Usable once per game during any combat. Roll all Munchkin d6. Add all odd numbers as a bonus to either side.
Munchkin Rainbow d6
Usable once per game during any combat. Roll all Munchkin Rainbow d6. Add all even numbers as a bonus to either side.
And of course you could implement a max bonus of +10, +12, or whatever seems most balanced.