Kindlegen's basically a modified mobigen, so you'll probably want a look at the old
Mobipocket developer site's docs on the format. One thing that you can apparently use in the Mobipocket reader that the Kindle doesn't do at all is border styling for anything.
Also, Amazon's DTP site has some stuff on formatting in its Knowledge Base. It's not much, but might be of some help.
Here's their
tiny page on CSS in particular and the
Formatting Guide in general. And the
Desktop Publishing Guidelines (3 meg PDF) which has a little bit on specifying font-sizes/text-indents/margins via CSS, along with the admission that CSS is basically not supported very much, or all that well.
Also, beware of the new Kindlegen 1.1 build 99, or whatever they're calling the latest. It's apparently supposed to have some fixes and feature enhancements, which as far as I can tell consist solely of removing the hidden -donotaddsource feature so that all the output is doomed to bloat.
And they still haven't visibly fixed the NCX thing where it looks like nested navpoints don't show up on the Kindle (although one can apparently get to them by navigating to any given navpoint at that level, and then flicking between them, but they're otherwise invisible and inaccessible until you stumble across one of them to begin with).