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I use the GTD method (or a variation of it).

Information capture happens in a variety of media and goes into a physical or digital "inbox". I have both kinds because sometimes I take a note with pen and paper, or I have business card, or I have my cellphone and I can take a picture.

My inbox includes the "pictures" and "downloads" folders on all of my devices. I link my devices together using SyncThing.

Then I have an org-mode file I keep my projects, someday-maybe's, and project archives in. My reference "file" is a 1/2Tb drive split into folders. My file organization is pretty flat right now, so at the top level I have "school" and "recipes" and "day trips", etc.

This is an utter cludge, but it does most of what I need it to. I've actually adapted it some to use at work and that has allowed my to stay very organized with work projects.