Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
allTags - allTags is a free, tag based file management application.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Tabbles - Tabbles use tags to organize and find files along with your colleagues.