It hurts my eyes when text is #000000 but maybe its because I have a really nice screen with high resolution. I understand it is about what works well but for some, above #000000 is much more comfortable.
If I find an article with #000 (or for example... HN comments) I can't sit and read them all at once, I have to go through them in bits and pieces and give me eyes a rest.
So if I want to be able to play games tweaked for this wide spectrum, and read text, I either just can't, or have to hope websites use grey-on-grey.
#000 is as dark as your screen is when the screen is turned off, which is not the darkest color that you can perceive. And if at any point it is uncomfortable to look your screen because it is blindingly bright, then the screen brightness is set too high.
White on Black (or Black on White) are generally bad. I prefer the low contrast in my example: http://codepen.io/anon/pen/ZORWRv
Though even the "medium contrast" is much easier on my eyes than default.