I forgot about Scarlet Witch. What could match her powers???

Just throwing this out there , if Mr. Manhattan can control all matter, doesn't that mean Casper (or any ghost) can show up and kick his ass?

True, which is why Superman never loses like that to Doomsday ever again, since he has too many advantages and admits that he didn't use them in their original fight.  Doomsday may be able to jump around (just like Hulk) but he still can't fly.  And yeah, Prime is a villain, but he's not really pure evil, he's more of a whiny sad jerkwad.  I mean, he's more for himself than anything.  He takes care of the Anti-monitor when he doesn't like how things are going. 

Superman.

DC have been known to hire 10 year olds to come up with the most ridiculously unstoppable list of powers for their heroes at times.

I can bench a quintillion tons no problem.

To me it is Superman. Before the nerf.

Silver Age Superman (a.k.a. Earth-One Superman): 1956-1986
His powers was at godlike levels before they depowered him to make more interesting stories :(

depowered list:

Could not extinguish stars.
Could not travel through time.
Could not travel at speeds faster than light
Had limited super-hearing abilities.
Could not move planets.
Had lessened invulnerability
Could survive in space with no oxygen for a limit period of time

Superman's weakness....yellow sun supernova. Deal with that.

Thor

Don't agree with the Dr. Manhattan, his powers place him as the most powerful being in the Watchmen universe, but he hasn't shown anything really all that special. Reality warpers have been shown to do more than he has.

Underdog.

About the only thing more powerful than Manhattan is whoever is wearing the Infinity Gauntlet. I can't remember if any heroes have worn it, though... Obviously Thanos had the most time with it.