I also use the site-designer method. I further divide it like this:
Free - site - designer
Stores - site - designer
so that when my friend and I have a mini-crop, I can easily tell her where/how I got the kits, so that she can get them too!
If you are looking for a way to organize by paper, colors, themes, etc then I
highly recommend ACDSee. I
LOVE it!
