I use Skim together with Bibdesk for all of my research, but I am keen on reading papers on my Kindle (e.g. on airplanes).
I would like to be able to convert annotations made on the Kindle to some that show up in Skim and Bibdesk.
Note: You can now get Kindle annotations through the web. So that might be an approach if the format that the Kindle uses natively is too obfuscated.