I really like being able to use footnotes, which unfortunately don't work well with Kindle-style flowing text.

I find it useful to explain some concept that most readers probably know, to bulletproof ("yes, I'm well aware there are one or two edge cases but they're really not relevant in general. Let's move on."), historical digressions that aren't important to the general point, and references. (Of course, if it's only references, those work fine as end notes.)