Personally, i'm used to using a version control system, nowadays use Git.
The Arduino IDE creates new subfolders under my ~/sketchbook, and it seems the most sensible idea to initialize a git repository for each of these directories.
I don't know if Arduino IDE ever creates more than one file though...
I also would like to use some program to document the electronics for my Arduino projects.
Unfortunately Fritzing uses a binary file format (a zipped XML), and these are a little unconvenient with version control systems.