Yesterday I learned about Bookcision, which is a bookmarklet that can extract all your Kindle notes into plain text files. It's not perfect (I wish they offered some configuration, and it relies on Flash for clipboard functionality) but it does what it claims to do!
@darius see also: kindle-to-md (my kindle to markdown python script!)
https://github.com/cblgh/kindle-to-md
it munches a kindle's clippings file and poops out a few markdown files indexing the highlights according to authors / books :3