Nice article. I find that Evernote serves my needs, but clearly there is room for a much more creative approach to knowledge management.
In any case, I wanted to mention a mind mapping application, The Brain (www.thebrain.com). I haven’t used it and it’s not open source. It’s actually fairly expensive. It does appear, however, to be much more in line with what you are thinking than a typical mind mapping application, so perhaps it will provide some ideas.
Another thought is that someone with programming skills should be able to leverage an open source networking tool (e.g. Gephi) as a knowledge based application . One site that has an interesting approach to networking tools is Six Degrees of Francis Bacon (http://www.sixdegreesoffrancisbacon.com/). A related approach is Debate Graph (http://debategraph.org/Stream.aspx?nid=61932&vt=ngraph&dc=focus). I don’t think either of these have truly explored the possibilities and they probably are not where you are headed but perhaps they can provide an idea or two.
In any case, best of luck.