Mind Mapping software is good, but for most things, you're better off throwing together a personal wiki using something like WikidPad, Zim, or Cherrytree (none of which require a webserver). For most applications, you care more about the information in individual items than about all of their relationships. If the relationship is really the important part, I'd personally use graphviz or something, but it depends whether you prefer to work in a WYSIWYG environment or with markup.