In relation to the last post, I've read Watchmen 3 times through now (Then lent it to Mark M.)
(Warning, Spoilers:)
Watchmen, to me, is about morality, and the concept of good and evil. Watchmen gives us a few, very opposing, ideas of good and evil, through several characters.
Ozymandias, the "villain" embraces the "Ends justify the means" concept. He wants the very best for humanity, and feels that he is the saviour of humankind. He actually looks down upon the rest of man as needing a guiding hand, and not knowing what is good for them. This wears on him, and it shows through the comics. What he's doing is right, but the steps towards it pain him.
The Comedian, who is explored through flashbacks, is nihilistic and cynical. He "gets the joke" as Rorschach says. He knows that the common person needs a figurehead, someone to rally under. As long as he does token "good" acts, he will be embraced by the American people. "Good" for the comedian is only what is in fashion at the time. His personal actions are otherwise deplorable, he raped a fellow crime-fighter, as well as murders a pregnant woman.
Doctor Manhattan, the only real Superhero in the book, is utterly unconcerned with humanity. He's incredibly fatalistic, paralyzed because of his ability to see the past, future and present together. He sees humanity as unimportant, his only ties to it being emotional connections with a few select people. Morality and any concept of evil or good are entirely unimportant to him.
Rorschach is one of my favorite comic book characters. He's an sociopathic, right-wing, conspiracy nut. Evil must be punished in the most harsh way possible, even if it means torture and murder. Rorschach stands for a very different "truth, justice and the american way"
On the whole, The story of Watchmen serves simply as a device to explore the characters. The characters themselves exist, more or less, to explore morality, good and evil, and the entire concept of masked superheros.