Last week the first public beta (version 0.5) of Paperpile was released (available for Mac and Linux). Paperpile is a desktop reference manager with typical features: search in PubMed, Google Scholar or ArXiv, import PDF files, support for BibTex and other standard file formates, etc. Paperpile currently doesn’t sync with a web-based version, and Paperpile doesn’t insert citations into manuscripts.
What is interesting about Paperpile is that the source code is available at github (using the GNU Affero General Public License). Other reference managers that make their source code available include Zotero, JabRef and Connotea.