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.

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.