There is a large part of me that despises the fact that the big blue guy is in the main continuity of the DCU. Seriously. I'm not Alan Moore, but I'm sure he's no fan of the idea. Watchmen was meant to be a one-shot - which pretty much tells you why I have not included him on this list.
But let's look at this. What we know about Doctor Manhattan is that he's a pretty dispassionate entity. He doesn't lose his temper often and, outside of seeking knowledge; he really doesn't care about anything. An indifferent god really isn't a threat to the universe at large - after all, that's what we have now.
Let us also examine what we know about Doctor Manhattan and how he observes reality. While there is a human element in the ghost of the man he used to be, his perception of reality really focuses on the big picture. He observes his entire timeline as an outside observer, choosing which part to discover at any particular time. On the one hand, we can say that he definitely is an all-powerful god - on the other, he is the slave to his own destiny and how the universe runs his life. A prime example of this is when the Comedian killed the Vietnamese woman he impregnated. When the Comedian killed her, he accused Doctor Manhattan of doing nothing when he could've prevented the shooting with his power. Manhattan knew it was coming but could not stop the action. Ergo, he must obey how time-space events play out.
While Manhattan is all-powerful, I don't believe him to be a threat. Much like the all-powerful Spectre as the wrath of God is a threat.