Sometimes I have a file in the project's top level directory explaining what the subdirectories are.
Or if I have five or six scripts which accrete over time with data going in one end and coming out the other end, I write a file explaining how I do it, before my shell history disappears and I forget.
I go with Ubuntu's default Music, Videos and Downloads. The other high-level directories are a development directory, a work directory, a personal projects directory, a personal directory, a development scratchpad directory, a things-to-do directory, and an old accumulated junk directory.
The development directory has some binary packages, git repositories, development journal notes (not on my blog), as well as some notes on aspects of languages and frameworks.
The development scratchpad directory has subdirectories by date. Mostly for code I am writing.
My work directory has all work information.
My personal projects directory has tax info for my S-corp, bank information, as well as information on personal side business projects and code.
My personal directory has my resume, contact info for friends and family as well as pictures of them, personal tax info, and this sort of thing.
I also try to name directories, and sometimes files, so I can find them with locate.