I have been investing quite a bit of time lately looking at various tools that can help me better organize and correlate information. In the mind mapping camp, FreeMind is making a concerted comeback after a period of arrested development since the last major release in 2005 (v0.8). The new and upcoming features are quite impressive for an open source development, and FreeMind may yet rival more professional tools such as MindManager.
One of the interesting features in the current version of FreeMind is the ability to publish interactive mind maps onto web pages using a Flash plugin. The FreeMind wiki contains a gallery showing many uses of mind maps rendered with the Flash plugin, and I have added a map I brainstormed on Issues in Publish and Subscribe systems for content distribution (this is a biggish map so right click the central node, selecting fold all from Node, to start from the main topic).
I often use mind maps as the first stage in defining the scope of a risk or threat assessment. There are several interesting examples of security mind maps available on the web on including threats to mobile devices, ISO17799:2005 areas, general IT security, and a colourful map on password awareness.