I organize by designer.... i used to organize by shop, but then I started finding that designers sell at multiple sites. I do recommend that if you end up organizing by theme, etc., that you make sure that the designers TOU stays with the kit so that you're able to give credit when you design with their items. I have found that some kits don't even have a TOU, nor a preview page with their name....and I have a small handful of kits of which I have no idea who designed them. These would be for free kits that were awesome and downloaded. I agree with the commenter above who stated that she saves her collab kits separately. I do the same....
I always make sure the preview is the first file listed within the sub-folder, if the designer hasn't set it up that way, there for I can see it right away and determine if I am going to want to use that kit.
I asked a bunch of folks when I began how they organized their files, and I just found that I had to do what worked best for me.... i admit that it is hard to find a particular item when you have more than 500 GB's of stuff! :-) However, I have a fairly decent memory of my top fave designers work and I know where to go to grab stuff most of the time. The other times, I find it's quite fun going thru my stuff to find the PERFECT element or paper, etc.
I know I probably didn't help you at all, but I remember having this same question so I would be remiss if I didn't throw in my 2 cents. :-)