Only character I can think of who might be able to stand up to him pure strength wise is the ultimate Gurren Lagaan that could throw Galaxies.
Also if I remember correctly at the end of the Buu saga they hinted that Goku could go to levels beyond SS3 but he didn't want everyone to feel bad, so SS4 could still theoretically be factored in without actually acknowledging
Goku IS in fact a Deus ex Machinaesque character through out the series Dragon Ball Z, which starred the Z warriors not Goku. (That's why it focused on the progression of their lives and powers not Gokus training in other world) Regular Dragon Ball was the series that showed the life story of Goku and that's why not much changes in his life from the end of Dragon Ball to the end of Dragon Ball Z.
By the end of the series Goku actually did have all the powers of a god in that he could sense anything anywhere in the universe (omniscience) he could then proceed to be anywhere in the universe that he so chose via instantaneous transmission(Omnipresence) had an infinitely immeasurable amount of power (Omnipotence) and was able to forgive anything (Omnibenevolence)
Superman, or any of the cosmic super heroes, wouldn't be able to defeat Goku in that not only would he be as powerful or more, he was also trained to be a fighter, he knew martial arts and how they worked (The only super heroes I can think of that were actually trained for combat were batman (who would lack the power to phase Goku,) and.... I can't think of anyone else, wonder woman maybe? Plus, he could just teleport any of them to hell and leave them there if he so chose.
The only thing Goku had going for him was that he was flat out over powered, and he REALLY had that going for him. Also, Goku did kind of have a kryptonite in his whole Omnibenevolence theme, that would be what got him screwed over most of the time.
