For STLs, each project has its own folder in a bigger STL folder. After doing this for ~7 years it’s a mess. That said, I very rarely print something again a few months later. When I print the first part I generally know how many I’ll need. I’ve been questioning my STL retention policy as of late. If I don’t ever use them again, why keep so many?

For my designs, and remixed CAD designs, I rely on fusion 360’s cloud storage. The search works well enough for me to find what I’m looking for without the need for further organization.

If I were to implement a folder structure, I would probably functional organize prints. Examples could be kids toys and their parts, gardening stuff, loudspeakers, robotics, etc.