I'm a huge fan of Watchmen, I will be seeing it later on today.
I gotta say, if you're going to watch a movie based on the fact that there is a few shots of a penis, why dont you just watch porn instead? You can see all sorts of penis' then, without the need of a storyline etc. Best of all, you can see them online for free, saving the price of a ticket! If you want them blue, then you'll have to get busy with photoshop.
Oh and just to be a total nerd - Dr Manhattan isn't naked throughout the whole movie, he works various degrees of clothing but he is naked in parts as clothes are a "human trait".