Many notes are easily organized -- when I take notes on books I am reading, for example, there is pretty natural connection to where the not should live (e.g. /education/books/design_of_everyday_things.txt)

Otherwise, since these notes in the context of a project, I can treat it the same way I treat code. So a mix of multi-file search, and directories that correspond to the knowledge in them (e.g. "finances/investing.txt" or "journal/happiness_project.txt", the latter containing any work I do on http://diurnal.st/2013/05/27/training-your-brain-to-be-and-s... -- which I don't do everyday by any means, but that's an example of the kind of thing that exists in my notes)