What about 1000 black holes?

You don't think Duperman can't resist that?

Irrelevant, because Nurse Bronx cannot do that.

Depends how hard Manhattan decides to crush

Manhattan could teleport "Duperman" into deep space (like, inbetween galaxies, not just inbetween stars) where he wouldn't be able to recharge his powers, and any time "Duperman" would try to escape, he would just have to think about him returning, and he'd be teleported back. After a while, "Duperman" would run out of solar energy and Dr. Manhattan disintegrates him. Fight over, nothing "Duperman" could do to stop it.

"Duperman" couldn't even put a scratch on Dr. Manhattan.

The writer would have to rely upon some extremely clever, or extremely shoddy cheats for Superman to win in a "fight" with Dr. Manhattan.

Ex: Something in Kal-El's Kryptonian physiology makes it impossible for Dr. Manhattan to molecularly disassemble him with a thought. If not, that's how such a contest would play out.

Ex: Superman flys around with tachyon emitters or lures Dr. Manhattan into a preselected area surrounded with tachyon emitters to prevent Dr. Manhattan from knowing his every move before he does. Example taken directly from Watchmen, which really only begs the question why Dr. Manhattan didn't simply disable the tachyon emitters. The answer is presumably he didn't have to, or he was simply too enthralled by the novelty of not knowing everything in advance for the first time since Osterman became Dr. Manhattan.

I could go on, but essentially Dr. Manhattan is a god in the truest sense of the word: he can make life out of nothing. He can turn matter into energy and energy out of matter. He could presumably create his own universe if he so desired.

What about a black hole comprised of kryptonite?

yeah and thor is a god and still gets his ass whipped by superman. dr manhattan cant mess with superman atoms anyways because of supermans bio electric field. this contest is a draw

You mean the bio electric field that Dr Manhattan can control and harness as easily as the atoms that make up Supes? It's an energy field. Dr Manhattan has control over such things as easily as anything else.

Secret Wars, a new one. Have a look up of it, it's not very good. I'm dropping comics after for a bit I thinks. 

The idea Supes can resist a god like being changing his very being is stupid, it shows why Superman is so rediculous.

He survived being turned into an inanimate object? I don't think survive is the right word you are looking for. Was he turned back or is he still a teapot?

Is that bio thingamagic still canon? you know, with the new 52 a stuff... or did they drop that and go back to being stupid?

bio field is just that, a field which can be manipulated.

Actually, lets just stop with the manipulation on superman and just have manhattan transmutate the battle field into a huge chunck of kryptonite and then proceed to raping superman in the ass with his blue pennis :p

You know what, I take back what I said about the draw. Superman wins.