Then you might be interested in VYM. It's a tool I've found few days/weeks ago, native program (no scripting involved, neither python nor EcmaScript, which is refreshing), C++&Qt, does not forces the user to have a mouse.
So far, I like it, I use it to note my thinking about few stuff, and it's proving quite helpful to know what I install on my systems, why I did so, what other solutions I evaluated, and how to configure them. I also use it in another, unrelated to nix, context.

[edit]
After having following prev link, it seems that vym is in there. I do share the "all mind stuff can't be a tree", but currently VYM can have 1) multiple trees per doc and 2) link stuff together like if you were "placing ropes between branches", but the UI on that is not really easy to use, unlike for the rest of stuff which is pretty easy to work with.
I'm now using VYM more and more to describe projects as it's much better than a readme.