2 contradictory thoughts:
Idea 1) If you can search on contents, why organize them at all?
Humans build elaborate folder trees to “organize” their stuff mostly because they can’t search on content and so they must be able to search on name and / or location. Breakking things into categeories matches well with the human associative remembering system. And the tree method of categorization gives a lot of pruning per layer, so for example with 10 folders with 10 subfolders with 10 files you can find one file in 1000 by only making scans through three lists of 10 items each, choosing the best at each scan. Hence folder=category trees are ideal for large collections of items that each fit into a single pigeon-hole.
But they’re notso-hotso for things which have complex content which straddles borders or inherently fits multiple categories. Like books.
Given content scan (Windows search, Google desktop search, etc.), just let HAL handle it. Certainly giving each book a meaningful title helps the scan too.
For file system performance reasons, I’d limit the size of any content folder single to around 1000 entries, and simply start another content folder alongside the first when it fills up. Put all of the content folders in a single container folder, and search from the container folder downwards.
Idea 2) Use either the Dewey decimal system or the Library of Congress. Folks who’re expert at cataloging knowledge and organizing it into categories have spent a lot of time refining those systems. Any home-brew system you’d come up with will become a mess if your interests are wide-ranging or evolving over time.
Given that, I’d make one folder per top-level category, say “Dewey 100 - *official category name *”(whatever it is), “Dewey 200 - …”, etc. Then I’d move each book where it belongs based on it’s 1st Dewey digit.
Any “Dewey x00” folder that had more than about 20 books would get a set of subfolders “Dewey x10”, “Dewey x20”, etc., and I’d move all the books into the right subfolder based on their first 2 Dewey digits. If I only had 20 books in say Dewey 300, then I’d leave that alone.; no reason to expand that in to Dewey 310, 320, etc.
This gives finer-grained organization where needed, but doesn’t burden you with busywork hyper-organizing your sub-collection of 3 books on dog grooming. It also means your collection slowly gets more organized as you go along, no matter how long it takes. ie I’d move all the books based on first digit before I began working down into 2nd digit on any of them.
For books which fit more than one categery, at least in your opinion, you can supplement the official cataloging decision by adding shortcuts from other places. eg a book about Einstien & his discoveries that the Powers that Be have cataloged as biography but you think of as Physics. Put the book under Biography and add a shortcut to it under Physics.
Even if you’re not an expert on Dewey cataloging now, you will be when you’re done and you’ll be able to rapidly get to the 650 series when yuo’re looking for books about whatever the 650 series is about.
This is even easier if the books you have already have Dewey or LOC numbers assigned by the publisher. Then you don’t have to make the tough decisions n where to put them.
This way you can also look the books up in online catelogs from any number of public libraries just for the purpose of seeing the Dewey/LOC number. This’ll make it easy for you to catalog them at first, and also easy for you to retreieve them later, using the public catalog as if it was catalog of your private stash, just polluted with a lot of extra entries you don’t own.