@jonie: I maintain the Annotations plugin. For Kindles, this reads the My Clippings.txt file and put this into a column in calibre for the books. I haven't heard that annotations for PDFs are not in the My Clippings.txt file. That might just mean that the people who use PDFs already know that they don't appear there. I'm not a Kindle user, so I can't test myself.
Kindle does store the annotations in other files. From a little looking a while ago, this would be a better place to get the annotations from. But, either the format isn't known or it encrypted somehow. I can't remember off the top of my head, but my memory was that it wasn't practical to use for this purpose.
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