With the ability to know everything, be anywhere, do almost anything and come back from anything Dr Manhattan is as overpowered as he gets though lack of showings previously kept him rather low. As of Rebirth, he has revealed to have been responsible for creating the New 52 Multiverse along with stripping away a decade of history as well as killing Pandora, trapping Mr Mxyzptlk and rewriting multiple timelines. He is also implied to be more powerful than even Darkseid himself.
I don't think there was any doubt Spectre is the most powerful superhero in all comics. With the Presence backing him up, the Spectre can't possibly lose unless plot devices were involved. He casually banishes 5th Dimensional Imps and handles threats on the scale of the Anti-Monitor, Zero Hour Parallax, Emperor Joker that threaten the existence of the DC Multiverse.
The most powerful superhero of the Valiant Universe.
The Phantom Stranger is nearly as powerful as the Spectre and is able to fight evenly with the Wrath of God but rarely goes into battle unless the Presence allows him to.
The Hourman of DC One Million has great mastery over time plus wields the Worlogog.
This young reality warping girl of the Wildstorm Universe
The original Dr Fate was powerful enough to give the Spectre great battles.
Though his power levels may change from time to time, however as the Sorcerer Supreme, Stephen Strange is no stranger to threats far bigger than himself, threats no one would want to handle themselves.
The Green Lantern of Earth 2 wields the power of the Starheart, the entity from which is the embodiment of all magical energy in the universe. He is one of the most powerful members of the Justice Society having soloed the entire DC Earth heroes, mentally possessed some extremely powerful individuals, fought Nekron and his army in the Underworld alone and closed multiple dimensional rifts. In the New 52 DC Universe, Alan Scott is connected to the Multiversal Green, powered by his avatars from multiple universes and is the only being who can fight off the invasion threat of Darkseid.
As an avatar of the Source, Takion is nearly as powerful as the likes of Darkseid and is able to do almost anything with his powers. Takion can manipulate the Speed Force, Quantum Field and Emotional Spectrum.
Even as a child he could repel himself from Celestials. Once as a grown up he could meddle with them like toys. Franklin has used his reality warping to bring a dead Galactus back to life.
From the Vertigo Universe, Tim Hunter is essentially a magical version of Franklin Richards.
As long as his multiple personalities are intact, Legion is a universal powerhouse.
He can trap the Phantom Stranger.
The power of a billion exploding suns and potentially far more, Sentry has shown time and time again why no one should mess with him. The guy killed Molecule Man for goodness sakes.
His insanity is literally the key to how powerful he can be. Genis-Vell is comparable to Sentry in many ways.
Nathaniel Adam has taken on the role as the Dr Manhattan in the New 52 DC Universe. With incredible displays of godlike power, Captain Atom is one to be feared and capable of so much more despite his early appearances.
He was arguably greatest Green Lantern to ever live. In the New 52 DC Universe, his power continues to grow as he comes a White Lantern. Kyle Rayner holds the Life Entity and Life Equation with him. He is becoming one with the Source.
Nate Grey was born with so many hax abilities it's not even funny. He supposedly has much potential as Franklin Richards. His powers however do burn out as a consequence.
The mighty Norse God of Thunder has battled foes few heroes could ever dream of. When motivated enough, Thor shows the true meaning of a god.
The Swiss Army Knife of the Justice League is by far their most dangerous member who has physically and mentally handled them before.
He may seem weak but he's one of the few heroes who could ever give the Mad Titan Thanos a hard time.
One of the best users of the Power Cosmic. Norrin Radd holds great power in his hands, making short work of anyone who dares delay his quest.
Few people ever see Beta Ray Bill for what he truly is.
Kallark has the greatest physical prowess in all of Marvel and few opponents can ever stand up to his might.
His powers have been described many times as near limitless, only difference being that he's limited by the reach of his limbs.
