I absolutely love taking notes and organizing my thoughts. Over the years I've tried many different software applications for doing so, and many of them implement a nested directory structure, similar to a traditional filesystem. But I have yet to devise a scheme for organizing notes within this structure.

For example, I usually keep a document explaining how I've configured each of my computers -- what software I have installed and why, etc. And I have a note on what's going on in my garden, what I've planted, what I've tried in the past and how it went, etc. I don't know what directories each of these notes should exist in.