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.
Monkkee - Keep a private journal securely on the Internet – to provide a convenient user experience your...
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
The Guide - The Guide is a two-pane outliner - a program that allows you to arrange text notes in a tree-like...
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Scrapbox - A new style of note-taking that lets you create, discuss, and learn together in one self-organizing space.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .