I do almost no organising of my paper notes. The only thing I do is that I add a date to the corner of the first page of when I start making a specific note and I keep index pages where I list page/note titles (or topics, themes, not everything have a title) and a page number.

I often browse my notes even when I'm not looking for anything. I read what I've been thinking previously because that often sparks new ideas and thoughts.

One thing where I find pen and paper superior to digital is that it's easy to write in the margins, draw arrows and annotate. When I got my first iPad and tested out digital notebook tools (with stylus), I was excited about the idea that I can resize and move my existing drawings around.

Then it took me a few days to notice that I don't really ever need that. I don't need my "finished" notes to look tidy or good. I got over the need to have organised and structured notebooks and embraced the chaos.

I guess it's different things for different people. For me, the flexibility of paper is superior to any digital solution because it has the shortest "input lag" or "feedback loop" to my brain. I'm happy to sacrifice other potential benefits for that.