I think that it's mostly due to genetics. I have friends who have stressfree lives, are remarkably healthy, eat extremely well, exercise regularly, and have absolutely beautiful skin - but they have dark circles under their eyes.
I'd say to make sure that you take good care of yourself and to focus on your better qualities. And don't worry about the dark circles if you do have them. I'm not saying that they are not a reality, but try not to let them overwhelm you. Stay focused on the positives and not this negative - we all have them in some way or another.