Ebook formatting is a lot like formatting for online help, with the added complexity of having to deal with the idiosyncrasies of various hardware devices. On Digital Book World, Kevin Callaghan provides some tips for making your ebook look great; for example, getting left-justified text to work (one of my pet peeves is how the Kindle defaults to justified text).
A simple example: try using a very light blue for a chapter title. How does it look on ian Pad and on a Kindle Fire? Probably nice. Now how about in night mode? Or how about on an e-ink device, like a Kindle Voyage? Is it legible, or is it too light?
You can use a media query to target e-ink Kindle devices and use black instead. But I would recommend just starting out with a color that works everywhere. Simpler is better when dealing with the large universe of reading systems, as you don’t know how many readers are still using Nooks or legacy Kindles. You don’t want their books to break, which a media query might well do (especially on older Nooks).