I'm happy to announce a new open-source citation manager called Paperpile,
based on many of the same principles that led to SyncUThink:
We set up a Paperpile-alpha Google Group
for interested alpha testers, and you can visit Paperpile.org to see when a public release becomes available.
SyncUThink uses a combination of web crawling and some clever regular expressions to find the PDF associated with your article and stores it back in CiteULike.
SyncUThink can download your PDFs to your computer, for easy offline (or e-book based) reading and annotation.
If a file has been modified on your computer, SyncUThink will re-upload the latest version. This way, your PDF annotations will stay up-to-date and backed up on CiteULike.
Some other useful info:
Libraries used: Processing | Apache HttpClient | JSAP
E-mail me with bug reports or suggestions: gjuggler [at] gmail