This spot could also go to Firestorm since they both have very similar power sets but Captain Atom wins out for two reasons. The first is for the fact that the character is the inspiration for Dr. Manhattan (more on him later), and the second is for the incredible fight between the Captain and Superman from Justice League Unlimited.
While we're on the subject of that fight, let's stop and take a moment to analyse it. During that fight we see Captain Atom's control over radiation by using his powers to mimic red solar radiation in order to hurt Superman, and if it wasn't for his durability being lower than the Man of Steel's he may have been able to walk away with the win.
Along with control over forms of radiation, Captain Atom has your standard superhero power lineup of super strength, flight and super speed.
Where things get really interesting, though, is his molecular reconstruction powers and his ability to manipulate his own density, allowing him to become intangible - not unlike Martian Manhunter.