Also, see here:
http://www.klippingskollector.com/
Quote:
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Klippings Kollector™ (Patent Pending) imports highlights & notes made in your KindleŽ to your computer and rapidly tags, sorts, organizes and prints reports on key people, events, vocabulary, quotes & far more!
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I know that it works with non-Amazon mobi books, but I'm not sure about the extent of personal document formats. You could ask on the forums.