Embroidery Library just had an outstanding tutorial on how to organize designs. I use that format because I like to be able to see what the design will look like. I use the categories that are used at that website, and have subfolders for individual designs.
I always print the color sheet before I embroider a design, and file it in a notebook. I make notations on it to reflect thread colors that I use, in case I want to repeat the design.
Here's the link to the tutorial:
http://www.emblibrary.com/EL/elproje...oductID=PR1735