Superman is so mich faster, stronger and durable. And I doubt that Dr.Manhattan is stronger than a Black Hole.

Dr. Manhattan, theoretically could create a Black Hole inside Superman...or turn his blood into Kryptonite.  Speed doesn't matter when you can not only move instantly, but exist in multiple places at once.  There are limits to Supermans' strength, also.  Dr. Manhattan could theoretically increase his mass to much, much greater than anything Superman could move.

That's the problem with this discussion, Dr. Manhattan simply isn't touchable.

Wow, Dr. Manhattan vs The Fenix would last forever. xD

It really boils down to a mental game. Dr. Manhattan just has to want to kill Superman and then it's instantly over. Up to that point though, Superman's only real chance is to find a way to manipulate Dr. Manhattan and have him disappear/end his own life/otherwise stop existing.

Unfortunately, Superman is not Oxymandias lol :D

All I know is that Batman would figure out a way to defeat Dr. Manhattan.

That's the problem. Dr. Manattan wouldn't know what Kryptonite is. And we've never seen Dr. Manhattan make a blackhole, so we can't assume he can. And I doubt that Dr. Manhattan can increase his mass to 5 Sextillion Megatons, which is a big feat for him.

lol, says who?  If Superman and Dr Manhattan exist in the same Universe, and yeah the same planet, exactly how would Dr. Manhattan not know about Kryptonite?  But yeah, nevermind that he could simply erase Superman, just erase him.  

'We've never seen' - That's why I said theoretically, you should study up on words.  We know he can control matter, at will, The Comedian says this to him just after he shot that pregnant Vietnamese woman in the bar in Vietnam.  He literally says he could've turned the gun into flowers.  So...yeah, he controls matter, ergo, can simply create a black hole inside Superman.  Oh yeah, and you do realize that he single-handedly was responsible for the surrender of an entire country.

You can doubt all you like, but we really don't know.  We do know Superman has limits, however.  So, it's kind of an unfair comparison.

EDIT:  Nobody's mentioned the two failings we know of for Manhattan.  Tachyon's can mess with his powers, and apathy.  He's generally aloof of human concerns, and basically just doesn't care most of the time.

List of powers:

Size Alteration, Godlike Strength, Teleportation of himself or other individuals over incredible distances, Matter Manipulation/Atomic Structure Control (Limits Unknown), independently acting self replication operating in an intelligent collective, intangibility, Atemporal (perception of time), Doesn't appear to age, doesn't require food, water or air, creation of environmental fields, can read atoms and sense tachyons, telekinesis, disintegration/Intrinsic Field removal (Unclear whether he's disintegrating his targets or removing their field.)

So, I guess the ultimate issue is his limits have never really been shown, so the argument is rather moot.

I think the real question we should all be asking is, who wiil win the goku vs superman dead battle part 2?

You've never heard of first encounters?

And that's the problem. Just because we've never seen his limits, doesn't mean we should make him able to do anything. That's a no-limit fallacy.