Brian McLachlan, creator of the webcomics The Princess Planet and Smooth 'n' Natural, recently wrote a wonderfully extensive (and illustrated!) article on how to color comics.
Comics is sequential story telling and therefore its primary goal is not making the nicest picture – its about making the clearest picture to illustrate your story. Just like you don’t draw every hair on a persons head, every pore on their skin and every leaf on a tree, you need to make decisions about what colours you will and won’t include.
It's written primarily for comics creators, but readers (and someday-readers) should give it a look as well. Comics gain a whole new level of enjoyment when you understand exactly what an artist has done to make their work look beautiful.