EndNote is a reference and full-text organiser with a collaborative Web tool:
(Software licence available for the U.Porto community)
Mendeley is a system that supports the management of bibliographical references. It collects and inserts citations and bibliographical references. It can also be integrated within word processors. The (free) desktop version allows you to use Mendeley offline and it will synchronise automatically when connected to the Web. With this tool, you are also able to import bibliographic references from databases and bibliographical catalogues.