implement an icon based desktop with links
Include an option to create a workspace with linkable objects (I got the idea in a dream from merging two ideas (http://brendangriffen.com/blog/gow-influential-thinkers/) and your background wallpaper you have on your homepage (http://www.tagspaces.org/).
One can link the folders/objects together (most likely based on the tags). That way one can visually organize their thoughts using a workspace (i.e. a desktop) with links between objects.