There is a well developed application called Klippings Kollector that you can find here:
and a reveiw:
It allows you to import your clippings (highlight and notes) via USB. You can tag your notes on the Kindle or in the software. You add comments and analysis, run searches and filters and print reports. It isn't free, but I have been having a great time with it, having bought it about a week ago. There are video tutorials on the website that will give you a fairly complete view of how it works.