I've spent the last few months designing an "academic workflow" for my PhD studies, which integrates BibDesk (for citation management), Skim (for taking notes and highlights) and my Kindle with a DokuWiki installation (which I run locally, and rsync to update on my server). I've written a ton of glue-scripts in Ruby using AppleScript to tie these applications together, and enhance the functionality of DokuWiki (and also a small plugin for displaying citations in DokuWiki, inspired by the refnotes plugin).
I made a screencast showing how it all comes together here, and have tried to document everything technical as well:
http://reganmian.net/wiki/researchr:start (and you can also see how the wiki looks - although as you see on the screencast there is quite a lot of functionality that only works on my local computer).
Stian