Outside of the Helicarrier i'm struggling to think how Hulk could hit Thor really. He's got at least bullet time reactions and has supersonic flight. Could whip up a tornado to keep Hulk off balance. Continuously strike him with lightning. Thor, if he plays it smart, doesn't even need to make physical contact with Hulk.
But if Hulk gets his hands on him and is fully enraged, i could see him pummelling Thor into unconsciousness.