I changed my system about 4-5 years ago - prior to that I was constantly trying to figure out how to find all my stuff in my stash and changed my system every time I tried to organize a big group of zips (so like DSD, iDSD, Black Friday, etc).
My current system I love, and I don't anticipate going away from it, is to organize by theme instead of by store - designer. My main categories are Colour, Elements, Theme and then templates:
Then inside the folders I name them kit name - designer name, and tag it with the store, and year, and that's it for tagging. That way I can search within a theme folder to see only things with a certain store. I added the year just last year, so I can know if something is really and I haven't used it yet I know it's ok to delete lol
Once I've used it I add z- in front of the kit name, so that it naturally falls to the bottom of the folder.
And similar with template - I only keep the tiff files, I rename them to Template pack name - Designer name, tag them with the same 2 things (store and year), and then I file them by photo spot:
I use the "z-" in front like I do kits, but also a y- to show I've got a started page with the template - something I learned from Reba.