These are all very good points, and I will admit that I don't know as much about Hulk as I do Thor. I like best what MSM said, though: "The problem with any comic book power debate is that every single character is subject to the author's creative liberty and time of publication."
If we look at the situation logically (what, logic? in a comic book conversation? madness, I know) we can come to my previous perception of Thor being the stronger. When I say that, it doesn't mean Hulk isn't a threat, but let's take a look at it a little closer.
Hulk is a human who's been tranformed/mutated by a gamma blast (comics origin), or by a super soldier serum plus gamma radiation (MCU origin). In both cases he is obviously vastly stronger than any mere human, but from a logical standpoint he is still, structurally, a human and limited by that fact.
Thor is an Asgardian Demigod. I actually don't like using the phrase demigod because it sounds like he's less powerful; in fact, his mother (comics origin) was Gaea, an Elder God. Because of this fact he is the Asgardian god of Strength, making him stronger than any other Asgardian. In comics form he's a god, in movie form he's the strongest of a race of incredibly strong aliens.
Without even giving him Mjolnir, Thor is, from a logical standpoint, the stronger of the two. He has access to the power of being an Odinson, meaning his regenerative power is equal or superior to Hulk's, and his strength is unmatched by any other Asgardian. Then you give him Mjolnir, a hammer with mystical elements and incredible hitting power, and you've got something that, on a base level, should be stronger than the Hulk.
That's just my take on the matter, though. Writers for both Thor and Hulk have gotten out-of-hand in their descriptions of how strong both characters are.
(PS: to brainfail: good points, except the one about Thor and Namor. Thor knocked a fully-hydrated Namor out with one punch in Invaders #33, apparently. But you're right: I shouldn't be trusting wikis :P)