The thing about both paper and Org-roam/Emacs, is that it's under your own control, and can be tailored to meet your own actual needs, not how someone else thinks you should do things. That's where Apple Notes etc. fall down.
Files are named hierarchically with periods. I have top-level categories that have changed little over the years. `con.` for concepts, `lit.` for documents, `proj.` for projects... you get the point, I'm not listing all of them unless someone really just wants me to.
My go-to example is always Star Wars. `lore.sw` is my top-level Star Wars note. I also have `lore.sw.chron` which is the chronological watching order. There's also `game.sw` which contains a list of Star Wars games I've found.
This extends to non-note files as well. For images of something I use `.img.[date].#.[ext]`, so for example I have some pictures of my cat named `ppl.neck.img.2024.03.15.1.raw`. I have a video of him murdering a bird too, `ppl.neck.vid.2024.05.22.murdering-a-bird.mp4`... As you can see, sometimes I replace the number with a nice title.
The modularity of it all is great. I can add anything anywhere at any point in the hierarchy without having to re-name things. I name things exactly what they are. The hierarchy can be sparse, parent notes don't have to exist. I can name something `stuff.something.i-dont-know.gif` without having any notes for `stuff.` or `stuff.something.`
I have notes on paper as well, and they use the same system, with the hierarchical name printed in bold at the top of the paper. `self.passwords` is a paper note for obvious reasons. I also keep most of my `sys.internal.` documentation on paper because my computer might not work when I need it most, though a lot of them do have computer versions which I just print out when I change because it's too much to write by hand.
agenda.: single file, my main TODO. I can also add `.agenda.` anywhere in any hierarchy to make a topic-specific agenda.
archive.: I just slap `archive.` on the front of any filename I want to archive.
con.: notes about concepts
cook.: my cookbook
film.: movies, shows, etc.. Contains both notes and actual films
game.: game notes, downloads, old versions, mod version archive, skins, settings exports, etc.
grp.: social groups, movements, governments, companies, religions, etc. Mostly notes from school and research from work, but some political stuff too.
home.: my house
inbox.: single note, anything can go in here for later processing if I'm feeling lazy
journal.: journal, organized by date (journal.2024.08.27). Hasn't been used in years.
lang.: languages of all kinds; spoken, programming, everything. There's `lang.lisp` next to `lang.latin`
lit.: literature, documents, etc.. Organized as `lit.author.series.document.chapter`. I have a lot of books.
log.: logs, never used this one actually
lore.: research about fictional worlds (I'm into worldbuilding)
meta.: about this collection
music.: playlist dumps, song downloads
ppl.: people
prod.: products
proj.: projects
school.: school stuff, organized as `school.institution.course.unit.chapter.assignment.document`
self.: me
social.: social media
soft.: software
sys.: my systems
veh.: my vehicles
Bonus: I also have `woodheart.` for my worldbuilding project, which contains a copy of most of the above categories within it.