Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Xmind - Xmind is a brainstorming and mind mapping application.
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.
FreeMind - FreeMind is a premier free mind-mapping software written in Java.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.