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Qiqqa is by far the strongest solution for research and managing pdf's. Zotero, named as a comparison is weak as it does not allow pdf;s to be loaded into its interface - you need to use a pdf reader, which defeats its whole purpose. With Qiqqa documents in a library can be searched together. It has excellent maps of your libraries. It is not prefect, having a few glitches, but still is the only one of its kind.
Xmind - Xmind is a brainstorming and mind mapping application.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Mindomo - Easy-to-create and share mind maps, concept maps, task maps and outlines. Mind mapping software for Web, Desktop, iOS and Android. Mind map with us for free!
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Freeplane - Freeplane is a powerful and free software for building mind maps.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .