I still haven’t found the perfect system for managing reference citations. Mendeley was close, but it is just too unstable for me. After having several crashes that caused loss of information in the database (usually, PDF links are lost), I decided to go with something text-based, where I have more control. Plus, I want to use something free. I’m trying out JabRef now.
A few notes:
It seems like the community is converging on DOI as being the central, important identifier for any papers (or other citable stuff). I’m really happy with the work of CrossRef and CrossCite, which I hope will continue.
So all I really need a database of DOIs, and then this can (programatically) convert them into whatever format I need. You can do it on the command line. This is what I used to in my JabRef pull request.
Also of interest: https://figshare.com/ http://www.carlboettiger.info/2013/06/03/DOI-citable.html