When my wife (then girlfriend) was doing her masters, I set her up with I, Librarian (http://www.bioinformatics.org/librarian/). At that time, it was (from the dozen or so that I tested) the best open source reference management software that I was able to deploy and make small customizations to. This was some time ago, nice to see the domain is still active.
As much as I used to like Zotero, I now use Mendeley[2], which has for better or for worse, been acquired by Elsevier.
[1] https://www.zotero.org/ [2] http://www.mendeley.com/