I would recommend sorting by item category and sub-category first, with subfolders for sites/creators, and sub-subfolders for individual creations. You'll end up with a lot of folders, but I think it makes it much easier to find stuff than if you have everything just jumbled together by creator, say (tried that once, and it got really unmanageable). I'm still in the process of putting it back together too, but my own Downloads folder looks something like this:
Build Mode -> DOORS -> Site/Creator -> Name of Door
Buy Mode
Clothes
Defaults
Genetics
Hacks
etc...
Hope that helps.
