My good NES games are on a different shelf than my not as good ones (though some average-to-good ones are on the "bad shelf" it's because the "good shelf" has really limited space). I do put the Konami and Capcom games next to each other, but that's about the only organization I have there.
On the SNES side, I have a stack full of RPGs, a stack full of shooters (shmup or run n' gun), and then stacks of "whatever, these are good". The "not that good" games are in a separate shelf, with all the "not that good" Genesis games. The good Genesis games are above the SNES ones, one side with the loose carts, one side with the boxed carts.
Everything else is by console, placed at random.