I'm not really an organization queen, but here is what I have:
Folders for stores, with kits from that store inside. I usually name the folder : designer name_kit name.
I have a folder called Kit Previews and when I unzip I also put the kit preview (a copy) in this folder, renaming it store_designer_kitname so I can find the actual kit.
Now, I also have a few folders for individual designers (not that many) if I got their stuff without needing to remember the store where I purchased it. I don't do blog trains much, but they have separate folders also.
I have a big folder called Kits by Season and I arrange my mini kits/freebie kits in there. I don't get into that one often. But it's there.
After I unzip, if I have time, I go in and take everything out of all the subfolders within a kit, and use just three folders: elements, papers, alphas. THAT is a pain, especially with a blog train or store mega, but I can't STAND all the little folders.
I scrap within a kit, so I don't really feel a need to organize any other way, or to tag in an organizer for easier searching.
Having said all of that, designers move around in real life, but on my hard drive, they stay with the store I originally put them with.