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Roamresearch and Obsidian are just two of the latest examples of note taking and note organizing applications that focus on atomic and networked notes. I'm tinkering with Obsidian because it does its thing on top of a local folder of markdown text files. (Before that: nvAlt)

One often referenced example from before computers is the Zettelkasten created by German sociologist Niklas Luhmann. He built up a collection of 90,000 handwritten A6-sized notes using a self invented numbering and linking system.

Here is a video recording of a presentation that details the structure and inner workings of Luhmanns Zettelkasten In German.

The book How to take smart notes by Sönke Ahrens is a good manual for applying this way of personal knowledge management (PKM) to your own work. Or check out this video to get an idea.

Harold Jarche has an online workshop Personal Knowledge Mastery that is a very gentle and thorough introduction to finding your own approach in this kind of working, and more importantly: thinking.

The real treasure trove with many historic PKM examples is the Taking Note blog. No new posts there since 2018 but with an extensive archive of posts going back to 2007. All kinds of goodies like how a 18th century poet did version control to (of course) common place books or medieval notepads.