Not quite sure if you really want that: open your favorite shell, and count the number of files in your data directory; then multiply it by, say, 2 seconds each -would you like to spend that time on organization, or rather making money? (obviously you can apply the same label to multiple files, but you still need to figure out what belongs to where).

Personally, I gave up on manual organization of my file system last year, and learned how to love built-in search. This works great, as the rough index is in your head anyways, so you can just take a single token of the filename, type it in, and open it up; massively reducing both access time, and eliminating organization entirely.