Look. They're both super fast, but Goku trumps it with Instant Transmission.
They're both super strong, but Goku has fought and defeated entities that have the destructive force to destroy entire planets. When you have the ability to completely disintegrate MASSIVE CELESTIAL BODIES, it kinda trumps noble Clark Kents spectrum of punchiness.
They're both durable as all hell, but you don't need Kryptonite to kill Superman, as I've pointed out before with Doomsday. If shit hit the fan, Goku could even pop a sensu bean...but beyond that, he has multiple different ways he can amplify/multiply his strength...Superman is limited comparatively.
Even with projectiles, Supes has Ice Breath and Laser Vision. The ice breath would be a mild inconvenience, though the eye beams might be pretty good. Still, Superman has been seen to succumb to laser technology constructed by MANKIND. The Androids gave Goku a kinda-sort of hard time, but only because he had a heart virus (which he recovered from). No technology seems to even phase a Saiyan anymore...and the idea of Lex in a power suit making a difference against a Saiyan is kinda laughable...that would be like strapping a jet pack to Mr. Satan.
Point is, all signs would point to Goku being the winner.
...but I'm not gonna pull the cop-out "ughh, they're fictional characters, you can debate until you're blue in the face, wahhh" card...but I WILL suggest that both characters are the epitome of honor and good will and their respective universes. They would be more likely to team up against a greater evil than they would fight each other.
......Having said that....I still totally want to see an animation of them fighting, but done well. That would be amazing.