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Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Diigo - Diigo is a powerful research tool and a knowledge-sharing community
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.
WorldBrains Memex - Bookmarking for the power users of the web. A privacy focused extension to annotate, search and organize what you've seen online.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .