Thor wins, no doubt.
He is much more stronger/powerful than the Hulk.
How many times have he fought and defeated what might just be the biggest and most powerful "villain" on the planet, or to be more precise...around the planet?
He has beaten and will go on beating(Until Ragnarok where they kill each other) the Midgard Serpent.
He made Galactus flee after a powerful God Blast. He penetrated the armor of the Celestial Exitar. Though getting his butt handed to him Thor stood against Surtur the Fire Demon, Mangog(Sum total hatred of a billion billion beings), though with the Odin-Force he merely willed Mangog into nothingness. He has constantly proven himself against the likes of Fafnir the Giant and the Dragon. He overpowered the Silver Surfer and Warlock(A God in his own right) at the same time!
He fought and defeated Bor(Grandfather) when brought back by Loki.
When he gets insane he really gets insane, so much so that even Thanos stepped in to try and cure him! Odin thought he should die in order to save everything.
There are many great examples of his awesome power and unbelievable strength. He generally however holds back.
I see someone asked where it says he does so, one would think that it'll be pretty obvious in itself. He can't just go out and kill everyone he comes across. If he handled everything in that manner he wouldn't have been "worthy" to hold Mjolnir ages ago.
Perfect example would be Loki. The guy constantly attacks Asgard, Thor and even Odin! In all the battles they had he never really beat him that bad as to kill him. He did break his neck once and did in fact "kill" him once. He got himself banished from Asgard both times.
He'd not do anything to jeopardize the life of a mortal. Even after Iron Man cloned him and the clone went and killed and hurt people. Not even in that betrayal did he kill a mortal. He just pummeled him good but that was about it.
He has many many thousands of years combat experience, I won't say training, but actual combat! That against other Gods, Giants and other fun things.
The Hulk is no match. I'd even go so far as to suggest that Thor would easily "allow" himself to be beaten just to put an end to the fight. Why would he? He got himself beaten up just to help Hercules reclaim his confidence after which point they fought together against their respective opponents.
That in itself is what separates a God from a monster! The Hulk will try and keep on fighting no matter how many lives it costs or how much destruction he leaves behind him. Thor can go toe-to-toe the whole way, if he so pleases.
From the comics perspective Hulk only really has a great chance of defeating Thor when one condition is met. He loses Mjolnir and 60 seconds later turns back into the Host body.
Though I still think that's the stupidest thing they could ever come up with. Thor and the Hammer are one. Though I suppose that they had to put it in in order to have a real weakness for him, silly I know.
Thor does have more power than the Hulk, but Thor wants to beat the Hulk by out bashing him. Hulk easily goaded him to get rid of the hammer and then Thor cast it away. Thor is too prideful when it comes to the Hulk and this plays right into the Hulk's advantage.
He cares too much about the mortals on Midgard. He was goaded into it after the Hulk held a human hostage. Reading through the comics you can easily see how many times things went wrong because of mortals. Especially when it came to that silly "Jane Foster", hell even Asgard could have fallen as long as little ole Foster is alright...
Writer-editor Stan Lee described Thor's genesis, in the context of having been after the creation of the Hulk:
H]ow do you make someone stronger than the strongest person? It finally came to me: Don't make him human — make him a god.