To make if fair let's assume we are referring to the best versions of both: King Thor and the Gestalt Hulk. (Not the omnipotent version of Thor, that would be an obvious outcome.)
Speed and Agility:
Thor can cover distance on foot faster, is more agile, and has better reaction time than the Hulk. Aided by his hammer Thor can traverse vast distances instantaneously. Hulk can jump a few miles.
Intelligence and Cunning:
The Hulk (Gestalt version) is a genius. He isn't just book smart; he has insight and is quite calculating. Thor is smarter than average. As King Thor he is quite intelligent, but he still isn't on Hulk's level. Hulk also fights dirty and Thor does not.
Strength and Durability:
King Thor can lift hundreds of tons (its been observed) and can use various enchantments to increase his strength significantly. The Hulk once lifted a mountain wieghing several million tons. Although the Gestalt Hulk doesn't get as strong as fast through rage as the others, he does get there. (and forget that mindless banner thing where the Hulk gets so mad he turns into Banner, that was just bad writing).
Thor has diamond hard skin. The Hulk can instantaneously regenerate virtually any injury and is bullet proof.
Fightins skills:
Thor has more formal training and experience, but the Hulk is simply a mean, vicious, cunning fighter. About Equal here.
So Thor is faster and more agile. Hulk is stronger, more durable, and more intelligent.
King Thor could beat Hulk if he took him out fast. That is, if he was rational about the fight and didn't try to be "sporting" about it. If he simply knocked Hulk out of the Earth's orbit and into deep space the Hulk would suffocate. Hulk can't do that to Thor because Thor would just fly back, unless he were unconscious in which case he would also suffocate. If he gives Hulk the chance, Hulk will figure out how to kill him.
This one could go either way.