... until Manhattan simply breaks Superman apart on the molecular level and redistributes his particles into a red sun.

Yeah the version of Superman that was able to defeat Mandrakk or the one that was able to stop the Atmos universe from collapsing, I think not. 

So... Manhattan can't be killed by anything Superman could do (he could simply teleport, move his atoms, rematerialize if vaporized, whatever) and could simply shift Superman to anywhere he liked (or just rip him into several pieces... Superman is strong but there's nothing suggesting that Manhattan couldn't simply reverse the polarity of atoms and tear him apart) but Superman would still win? How?

The best you could argue is that Superman's molecules are too strong to rip apart and therefore, would stalemate with Manhattan. But beat him? No, not really. You can't beat a guy who can restructure his own molecular makeup unless you have a method of teleporting him to another dimension or something of that sort.

Hah, Reed Richards has turned into a dick over the past decade or so. It seems popular to write him as more of a hard-ass now than it was in years past.

I knew Warlock had the IG but I hesitated to call him a "hero". Like you said, he's kind of third party and does what suits him. Kind of a tweener character that can go either direction.

I was avoiding other dimensions' characters. Obviously with the latest storyline in FF, there are a shit-ton of Reed Richards, some villains, some not, all super-smart with varying levels of technology. Both the DC and Marvel universes involve too many variants to ever keep track of who is alive, dead, powerful, weak, etc.

For the life of me, I can't remember if the Surfer ever had the IG in this dimension. I should probably go back and re-read that era of SS some time. I used to love the character. If he ever possessed it, I think he's pretty much the most powerful character ever (in his dimension, anyway). The Surfer is already in the upper echelon of Marvel heroes; with the IG, he'd be unstoppable. There are only a handful of Marvel characters who the Surfer couldn't whoop without the IG much less with it. Plus, he has that whole "nobility" thing and the IG probably wouldn't reject him as it has others. He's also smart enough to wield it, unlike others who basically had their brain overloaded by the thing.

Well the version of Superman that defeated Mandrakk aka Cosmic (monitor) armor Superman was able to take hits from Mandrakk a guy that could destroy multiple universes and he could dish out even stronger attacks, there wouldn't even be a mollecule of Dr. Manhaton left. that version of Superman also held the power of being able to adapt to any kind of threat. Although if you wan't to argue that Dr. Manhaton would still some how survive, then Corsmic armor superman would probably send him to limbo.

Let me ask you a question.... have you read Watchmen?

It's not that Doctor Manhatten can destroy universes.

It's that he can make them cease to exist.

By the time you adapt to that... well you don't exist.

To quote watchmen "God Exists, and he's American."

Dr. Manhattan more or less represented a christ like god who was unstoppable.  

It's also worth noting, that unless your using a very specific kind of radiation.  Dr. Manhatten knows what your going to do before you do it, because he lives in all moments at once and can pick whichever future he wants.

Many character are seen as gods in diferent fictions, the question is whether they have the feats tp support their nigh-omnipotence. 

the bolded is a character statement and can be seen as an nlf. 

Cosmic armor superman has adapted to people like Mandrakk who are way above people like DR. Manhaton. Also I would like to see this feat by Dr. Manhoton of him making universes cease to exist and alo being omni-present.