Common things are simply by category and subcategories starting from the media/file "type" (e.g. books, photos, etc).
Projects are created in a ~/playground directory and are eventually moved to a ~/projects one (but sometimes they just stay in a RAM-disk; i.e. experiments).
Within coding projects I usually have /src, /doc (by category and subcategories) and /utils (with utility scripts, Docker-related files, etc) sub-directories.
PDF et similia that don't fit within a specific project typically are generic enough to be placed somewhere under ~/books.
The main issue with this system is that there could be work-related things under distinct paths (e.g. ~/documents/work/<org> and ~/projects/<name>), but those may be archived together...