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Altho Superman, as noted, does not have a SPECIAL vulnerability to magic -- ie, he is no MORE vulnerable to magic than anybody else -- where that vulnerability would manifest in a fight with Thor is that the magic in the hammer would have the effect of NEGATING Superman's powers.* So, as noted, the effect would be one enormously strong guy hitting another enormously strong guy.

In the case of the Hulk, however, the effect would be one enormously strong guy hitting ---- the Hulk! It would probably HURT a lot more than being hit by, say, a girder or a big chunk of rock, but it would not have the effect of placing the Hulk effectively on the same "plain" as Thor.

..

*This effect would be specific to the hammer. If someone was to SHOOT Superman at the same time the hammer hit, the bullet would still bounce off.

QUOTE: Reading this story, I remember having the feeling that Kurt Busiek didn't want to show his preference for a character over another, so it seems he came up with the idea that Marvel heroes are less powerfull when they stand on DC Universe's Earth and are stronger when they stand on THEIR Earth : that's the reason why, at a moment of the story, the Flash runs faster than Quicksilver because they are on the DC Universe's Earth and later, Quicksilver runs faster than the Flash on Marvel's Earth...

That's not the way it was, actually.  Flash slowed down on Marvel Earth because there is no Speed Force there, not because the DC heroes are all weaker on Marvel Earth than on DC Earth -- that's just not in the comic, though I have heard it as a heartbroken Marvel fan excuse (not saying this applies to you).  In fact, while on Marvel Earth, Aquaman of all people pitied its heroes as they were, in his opinion, less powerful than the heroes of DC Earth.  Powering down on Marvel Earth was unique to Flash -- happened to no other DC hero and happened to Flash because of the absence of his source of power, not simply because he was on Marvel Earth.

QUOTE: I don't exactly remember the story and at which moment Superman is hitten by Mjolnir, but I think it happens on DC Universe's Earth and so Superman is less vulnerable to magic on HIS Earth than on Marvel's Earth (or maybe the magic of Mjolnir is less powerfull on DC's Earth...)

Nope, Busiek simply wrote him as powerful enough to take Mjlonir's hits and put down Thor.

QUOTE: He came up with a good idea with Cap and Batman since they have no power: the two opponents start to fight and very quickly understand they have to join forces to understand what's going on and who is the villain behind the develish plan which led Marvel and DC heroes to fight ...

Yep, another crossover comic cliche.

If John Byrne wants to write a good story that ignores the whole "two Earths" nonsense and simply treats the heroes as if they had always been on the same Earth, and simply had not met before, I'm OK with that (and, IMO he has done so with Batman/Captain America, to pick one example). 

If Kurt Busiek wants to write a good story that does NOT ignore the whole "two Earths" nonsense, I'm OK with that, too (and, again IMO, he has done so with Avengers/JLA).