Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Weava - Workspace to highlight, organize & collaborate on your research articles.
Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.
Good Annotations - A online annotation tool that is perfect for providing feedback to your team.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
Genius Annotations - Embed text annotations on your site. Annotate the web.