When I first started scrapping I had everything on CDs/DVDs - that was a nightmare, because I had a DVD for each store, then files for each designer. when they moved, I was screwed. When I transferred over to an EHD, I went with folders by designer, then just dumped the kit or element pack folder into there.
The only extra thing I do is on my laptop, I have a "Saved Products" folder. It has folders for all my CTs (at this point only the Lilypad), then folders by element (papers, frames, flowers, etc). When I have used a kit and it's saved to my EHD, I delete any product I don't think I will use. Anything else gets moved over into my Saved Products folder. So then, when I need a specific element, like a flower or a piece of word art, I can go into my saved stash and pull a couple of needed items from there.