Having just finished reading the comicbook, I have to say I like the way the movie handled it. The old addage of "the book is better" certainly applies here, though.
*The comic grants a deeper look into the lives of the characters, especially Ozymandias. The movie touches upon his admiration of Alexander the Great and hints at his fondness of ancient Egypt, but the comic shows just how obsessed he was with these two things. Makes sense, given his masked name is the Greek translation of an pharoah's name, but hearing about his trips across Europe and Asia, the drugs, the early fights with the Comedian and the epiphanies that accompanied each was amazing. Also, when his plans succeed he shows a lot more emotion in the comic than the movie, though whether that is a good thing or bad thing is dripping with YMMV.
*Subtle things, too irrelevant to put in the movie, but show how well developed the world is. For example, the effects Dr Bluedick had on the world's technology - electric cars, airships, experiments in teleportation, etc. Also, I was particularly fond of how superheroes fell out of favour in the American public along with the real heroes, allowing pirates to rise as a dominate genre.
*Especially towards the end, certain choice quotes were either left out or butchered. Consider:
Movie
Silk Spectre: But I thought you'd regained an interest in life?
Dr [del:2e336qj7]Bluedick[/del:2e336qj7] Manhattan: Yes. I was thinking I'd go create some.
Pretty cool. He goes to another galaxy, shuffles some complex molecules around and a billion years later that world grows fungus.
Comic book
Adrian: But I thought you'd regained an interest in human life?
Dr [del:2e336qj7]Bluedick[/del:2e336qj7] Manhattan: Yes, I have. I think perhaps I'll create some.
Key difference, the addition of the term human. He'll create some human life? Perhaps a world similar to Earth, with people, but without the masked heroes, without a walking nuclear deterrent, with a Cold War which concludes naturally and peacefully. Perhaps he will create us.
Much cooler. Also contrast these lines:
Comic book
Adrian: Jon, wait, before you leave... I did the right thing, didn't I? It all worked out in the end.
Dr Manhattan: "In the end"? Nothing ends, Adrian. Nothing ever ends.
Adrain: Jon? Wait! What do you mean by ...
An ominous warning. Peace, even such a dramatic peace, is only temporary. Tempers will eventually reignite. He can, after all, change many things, but he can't change human nature.
Movie
No equivalent line
*But there is one thing the movie did brilliantly that the comicbook got snagged on. Genetically engineered monsters? Psychics? Bad dreams? Only New York targeted? What the fuck, comic book? Make more sense! Do it!