JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef runs on the Java VM (version 1.5 or newer), and should work equally well on Windows, Linux and Mac OS X.
BibDesk is a graphical bibliography manager for OS X, providing powerful BibTeX file management for Mac users. It is free and open-source. It is under active development by a small group of volunteer contributors and more are always welcome.
Sciencescape is both a tool for discovering and for organizing research. Sciencescape automatically scans, groups, tags, and categorizes research papers and you can subscribe to topics you are interested in. You can also create your own libraries to collect and organize key papers that you discover.