I have a folder on my desktop full of other folders, and some of those are full of even more folders. I put the books in the folders that make sense. There are ones sorted by game, by setting, by edition, by type (Monster Book, Player option book, setting book, etc.)..
If there is more than one folder a book could reasonably belong to, I'll just copy it and put it in both. If I find myself looking for a book, and going to a folder that doesn't include it.. I make sure to add it to that folder once I find it.
Far from elegant but it works for me. I also don't have that many books. Maybe two or three dozen.