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.
FreeMind - FreeMind is a premier free mind-mapping software written in Java.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
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.