Ok. For the ones saying pre-crisis would win, i think is only fair that we use goku shenron-fused. In that form he literally is the ultimate god of the anime universe.

If youre talking about after crisis boyscout, let me throw a few facts...

in that universe, the gods are called kai. Guess what? ssj goku is more than enough to take them out...supes can throw planets, yeah...just tell me where did he grab them...anyways, normal goku stopped vegeta's galick gun, which would destroy the earth. Hes can destroy galaxies you know..

Supes aint that invencible. Darkseid wooped him, doomsday killed him, and it was all physical attacks. Even though i dont agree, lets say supes is faster than goku. the thing is, he is that fast only moving, not fighting. Remember the fight wth doomsday? supes was afraid they'd destroy metropolis simply because of their bodies clashing....well, goku skakes the entire planet just powering up...

Since ki isnt magic, a super kamehameha would melt boyscout's butt for good.

But, for supes am not even calling goku, which like to play when fights. am gonna call someone even meaner, tough as they come:

ssj2 gohan (teen gohan) this one right here would woop supes non stop because he cant keep up with gohan's speed while fighting. laser beams..?

even chiaotzu's ki blasts are enough to counter that. Just so you know, goku was in hell and came back to tell the story.

All in all, supes doesnt have the battle prowess that goku has, and that alone will determine whos the winner. I mean, check supes adversaries..metropolis goons and once in a while some being worthy attention. goku is always battling fckuking bastards one-finger-galaxy-destroyers...