My members prefer dark skins; they all seem to be up at 6 am and light ones give them eye pain.
It depends how the dark skin was created. For example the skin called "AfterDark" by vBStyles is very easy to read and good on the eyes in both night and day. But in general some dark skins can be hard to read because they are too dark and use the wrong font colour etc.
A lot depends of the design with dark skins. You either get it right or wrong.
I find light skins hurt my eyes more than darks skins after a while, it's the brightness that gets to my eyes.