This one is tougher. Superman has alot of weapons (heat, cold, speed, strength) that he can use. Hes weak to magic (though Thors powers arent magical) and needs the sun for his power.
Thor has his hammer (which he can only use because his daddy lets him) and the ability to control lightning (powerful but not magic). Unless Thor can fight him in Asgard where Superman cant use the sun to rejuvinate himself, Superman is superior in all aspects and will destroy Thor.

Lol his hammer that his daddy gave him.

Good. Now do the Two Men Without Fear:Daredevil vs. Green Lantern! And if you are also doing Marvel vs. Marvel and/or DC vs. DC then you can do Falcon vs. Vulture for Marvel and Mogo vs. Ranx (Both from Green Lantern: Rise of The Manhunters video game) for DC. BAM!! Already got plans.