Watchmen co-creator Dave Gibbons said in a Q&A that he wanted Manhattan's blue skin to represent a sort of barely-contained "electrical energy or atomic energy" in the reader's perception.
Dave Gibbons: Actually, Dr. Manhattan is not the only blue character that I’ve created the look of. I co-created a character called “Rogue Trooper,” who appeared in the British weekly comic 2000 AD, and he had blue skin. Rather reptilian skin.
I like blue because it kind of reads the same kind of tone as skin, or as Jon Osterman’s skin would’ve read. But it’s obviously not real human skin. Green makes you think of bug-eyed monsters like aliens, yellow is too strong a color, red looks artificial. A light blue kind of looks like skin tonally, but looks completely different from it in its hue. I think it also relates to the way you might visualize electrical energy or atomic energy. That it’s a kind of blue, pure energy. A cold energy, unlike fire or flame, which is what a red color would make you think of.
That was really why I chose blue. I think I just came up with the color and Alan incorporated it in the story. It didn’t make a lot of difference in the story which color he was, but I think visually, that blue was the right color for him. And it worked very well with the colors of the costumes of the other characters, and also the fact that John Higgins and his color palette didn’t use a lot of blue as a background color. So I think for that reason, it worked.
Watchmen Secrets Revealed
That the blue glow was caused by a form of Cherenkov radiation was (to some extent) confirmed by Gibbons in a round-table discussion on NPR.
Dr. KAKALIOS: Well, yeah. Actually, I - see, I lost a bet. I thought that you had chosen blue for the color of Dr. Manhattan because whenever you see images of nuclear reactor piles underwater, you see them emitting a blue glow, and…
Mr. GIBBONS: Yeah.
Dr. KAKALIOS: …blue light is from the fact that they're emitting high-energy electrons which create an electromagnetic sonic boom called Cerenkov radiation, which is in the blue, ultraviolet portion of the spectrum.
If Dr. Manhattan were blue because he was emitting these high-energy electrons all the time because he had reconstructed himself atom by atom, well, he probably would be giving people cancers.
Mr. GIBBONS: Right.
Does 'Watchmen' Hold Hidden Physics Lessons?