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I'm not sure if it works for all Kindle devices, but I've seen some threads discussing a "Fetch Annotations" feature for Calibre that (at the time that the threads that I've read were posted) works for the Kindle 2.
I have heard that Sony e-readers handle PDF's better than Kindle, and I ran across a thread that was giving some very positive buzz regarding EnTOURage's PDF annotation capabilities. I've been told that you can "export" your annotations from those devices, but I'm not entirely certain what that means.
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