I organize my digi-supplies by Store/Designer too.
I will rename folders of things I have unzipped to fit my organization method.
I like to see alphas and collabs at the top of the sorting order. Collabs I will just put in the store's folder.
For my photos, I have tried lots of methods, but the only thing that seems to work for me is organizing by date. I have a folder for the year 2009, then folders for each month. When I upload images from my camera, I rename the files at that time to include the date info too -- for example, one of my photos from April would be 2009_apr_12345. This helps me because my dh has his own camera and it takes him forever to get them off the card and to me. When I burn my back up copies to disc, I know where to add his photos.