Speed is the one area in which Superman has a real advantage over Thor. Superman could fly around the earth and arrive back in the same spot before you would be able to blink. The only hero in either universe who is faster than Superman is (of course) the Flash — but while Superman has super speed, it's not like he would be able to catch Thor off guard by just flying at him. The comics have seen Thor detect incredibly fast moving objects, so he may still be able to see Supes coming.
Even with Superman's speed, it's well documented in the comics that Thor is able to throw Mjolnir at the speed of light, and his magical abilities mean he can also spin it at twice the speed of light. He may not be able to fly at the same speed as Superman, but the Man of Steel may have to watch out for flying hammers that pack quite the punch if he tries to catch Thor off-guard with the old "around the world in the blink of an eye" gambit.
Of course, one also has to factor in the fact that Thor has been protecting multiple universes from insanely powerful threats for centuries, and quite successfully, no less. His experience in combat would count in his favor if he were to be faced with fighting Superman.
All of these things considered, we believe there's only one reasonable conclusion to be reached. Sorry, DC fans, but it looks like realistically speaking, the God of Thunder seems to have an unmistakable edge over the last son of Krypton. That's not to say that Superman wouldn't put up one heck of a fight — but for our money, in this battle of the titans, Thor wins.
