For reading on a black background in the dark, I think an important distinction is between LCD and OLED. With OLED devices, the background is almost completely black--no backlight seeping through. (There is still a faint glow, but it's an order of magnitude dimmer than on LCD.) The only light is the text.
Personally, I reallly like reading in the dark with green text on a black background. :-) (Moonreader and APV PDF Viewer support green on black, and with other apps I can force that with my free GalacticNight on my phone.) But then I grew up with green-on-black screens.
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