Freeplane is a great mind mapping software. I use it e.g., to jot down and organize notes from articles I am reading, creating lists of software, relevant websites, etc.
One of the advantages of Freeplane is that you can export your mind map in many formats. This including different formats for online publishing, e.g., as java applet or a clickable map image version.The java applet offers a basic interface to your mindmap, including search and expanding / collapsing of the nodes.
For an example, see this mindmap on my ecodiv website. It provides a short list of some of the open source software I am using. I’ll probably add more to the list in due time. In the meantime feel free to suggest your own favorite software :-).