Sciplore MindMapping is an excellent software tool for researchers. Besides the ability to create mind maps of your brainstorming sessions, it allows linking nodes of the mind map with PDF files in your computer, import book-marks and references stored in BibTex format. Recommended for researchers in all scientific disciplines.
What started as a research project by the PhD students Bela Gipp and Jöran Beel at the University of Magdeburg, Germany in 2008 is a full fledged and still growing software tool and platform assisting research in many fields. Here is a little introductory video from their website.