I don't think I've ever actually read an issue where Hercules beats either Thor or the Hulk. He's fought Thor to a stalemate (which you would think would make him equal to him), and I don't know how he's done against the Hulk (though now that the Hulk is omnipotent, Hercules would get flattened, if not killed). I do think that Hercules has been shafted, but I guess that the level of a character's strength is always a function of his popularity, and his has never been that great.
Speaking of the Hulk, when the writers and directors give him limitless power and make him completely invulnerable, where's the challenge or drama in that? Just watching him pound one hero after another into the dirt and showing how everything bounces off him, issue after issue, should get old to most readers after a while. I mean, like in Hulk #5 when Thor smashes his mjolnir with all his might directly into the Hulk's face and he just smiles - c'mon, really. So much for the Thor/Hulk rivalry, eh?
IMHO, pretty soon sales for the Hulk should go down, since a collective yawn should go up when reading of how yet another Marvel strongman gets mashed by an angrier-than-he's-ever-been-before *yawn* Hulk.
I think the editors and writers have gone after a quick buck by all this novelty of the Hulk now being crazy strong, but it can't last. It reminds me of the DC editors, who decided they'd "kill of" Superman, knowing full well they were going to "bring him back to life" in a later issue (a fact they kept secretly under wraps). At least now would be a good time for there to be a DC-Marvel crossover, featuring the Hulk taking on either Superman or Wonder Woman. He'd fix their red wagons for sure.