They're mice. They fail every single time. Superman wins.
Pinky and the Brain could win in a fight against Superman.
Ambivalent to the fact that Pinky continually fails.
The Brain could come up with marvelous ways to get rid of Superman.
Possibly the most obvious way to get rid of superman would be kryptonite laced sunscreen. Weakens him, and blocks out his power source.
I'd like to say The Brain would have done a thorough background check on Superman and learned that he has a habit of escaping death. The only logical way would be to separate his head from his body. But, I can't see the Brain actually doing that and Pinky would be too squeamish.
So most likely he would transfer superman's powers via electricity to Pinky.
Which of course would be his downfall in the end.
Yeah I have to go for superman on this one. Superman isn't an idiot, he's not going to sit there and say "hey this sunscreen hurts like kryptonite" and keep putting it on. One of the great things about Pinky and the Brain is they always fail. No matter how far they take their plan it always backfires or they sabotage themselves.
Superman for the win.