Hey guys. I've tied together a bunch of applications (primarily BibDesk, Skim and DokuWiki in Chrome) to come up with a solution for managing and sharing citation metadata, notes, PDFs, etc for my academic readings. Part of the package is automatic syncing with Kindle - I can take documents in BibDesk and automatically send them to Kindle, reformatted and with nice metadata. I can then take notes and highlights on the Kindle, and once I plug in the Kindle in the USB port, it automatically imports all citations into the wiki, and attaches it to the right articles. (Here's an example of a publication that had its highlights automatically imported:
http://reganmian.net/wiki/ref%3Aallen2001getting)
I've tried to document it all here
http://reganmian.net/wiki/researchr:start
Stian