I looked into this in 2013. At that point there was a "My Clippings.txt" file stored on the kindle that was accessible as a USB storage volume when plugged in. This file stored each annotation in plain text, along with the document ID and the start and ending location of the annotation.

Trouble was, the location was in the Kindle's "Loc" format which is nontrivial (at least to me at the time) to connect to specific text in the document.

I'm sure someone's probably worked this out by now?

Update: yes, at least 160 projects

https://github.com/search?q=%22my%20clippings.txt%22&type=re...