Perhaps because Org-Mode just does the job of note taking so well, no further enhancements are needed?
Myself, I use it to document the work I do (so note taking primarily, some task scheduling and some project tracking). I put a single
file in a directory, then include excerpts from emails about that piece of work, links to scripts which run the various analyses with overview documentation mostly in the org file, excerpts of results, TODO/DONE items to schedule stuff that can't be done right away. Then I can create an html-export, and give my colleagues on the same project a link so they can always check up on where it's at, etc. These
files can get quite huge, and the outlining/TAGS functionality means they remain navigatable.
I hadn't considered concept maps, but see these could be very useful in the development stage of projects - thanks for the tip! I'm not clear, though, how these would work in org-mode (without export to graphviz or similar).