Way I see it is in the comics the Hulk is the stronger: Thor is usually presented as a little stronger than a calm Hulk, but once the Hulk gets his steam up he soon passes him. However, Thor can double his strength with his special belt, but afaik he has never used that against the Hulk (in theory as the Hulk gets angrier he could soon catch up and pass a boosted Thor as well).
And Hulk being the strongest is the way it should be for me, as strength is the Hulks only real power. That's one of the things that put me off reading Superman when I was kid (pre-crisis back then). He was pretty much a jack of all trades and master of all of them as well. I prefer to have that one guy who is the strongest, and another be the fastest, another the smartest, and so on.
Anyways, in the comics they usually have the Hulk coming out of the fights the better, but that's down to writers not having Thor using his other abilities (super speed for one), his belt, and all the various energy blasts the Hammer can generate. Thor using everything at his disposal could take the Hulk imo, but when they face off it is usually just written as a slugfest, which is obviously playing to the Hulks strengths.
For the movies we have not seen Thor really flexing his muscles without the Hammer so his inherent strength is still pretty much unknown. He is obviously gonna be very strong, but we have nothing to compare to the movie Hulk's feats. Personally I hope they don't sit on the fence and make it a bit vague as to who is the strongest. When they fight I want to see Thor genuinely stunned that a mortal can kick his @ss around.