Mindmapping is a great technique for visualising our own or group thoughts on a topic, and its relationships. Electronic mind maps can extend the typically manual mind mapping process with new capabilities. There are several opensource offerings which are particularly suited to the development and sharing of scientific and general academic research outcomes. Which tool is best for your purposes...depends...
Freemind, while not necessarily the first, is arguably the most well known and used of the mind mapping tools. It is stable software, and very usable with a drag and drop interface. It is not cluttered and while keeping a clean interface, provides facility for adding notes and export of outlines for document editing.
Freeplane started as a "fork" of freemind, offering several new features. While there are many differences, the most noticeable are seen in node styling and ability to have "un-connected" nodes
Docear is an academic literature suite adding the mind mapping from freeplane and the reference management in Jabref . Docear looks like a tool worth checking. There is a great "youtube" video which illustrates the Docear features.