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My current go-to organization system (for wallpapers and a number of other things) isn't optimized for already-huge collections but it might help.
I basically gave up trying to organize things perfectly because my categories never quite work when I set them up ahead of time. When I started my current sorting system I dumped all my wallpapers (maybe 100+ at the time) in an "Uncategorized" folder. I saw things that fit into a general category that I had a lot of in that folder, and moved those into a new folder - space photographs, for example. I had a bunch of sci fi stuff so I put all that in one folder. When one of these folders gets too big, or there's a subcategory I want easy access to, I split it off from the parent folder into a new folder for that thing. Mostly I break up folders that get too big, but sometimes I'll do it for small collections that I don't want mixed in with other things, like moving Halo, Mass Effect, and Star Trek out from the general sci-fi folder. Star Trek only had 1 pape in it originally, I just didn't want it when I didn't specifically want Star Trek. In contrast, my 40k folder is getting pretty full so I'll be making splits soon.
In short, start with one category, and make new ones only as necessary.
Hope that gives you some ideas. If not, enjoy the pape.
