Chris Aldrich provides a thorough run-down of various traditions of Commonplace Books and Zettelkästen, a valuable collection on the history of such concepts. It is extended by a view on the recent emergence of “Digital Gardens”.
In the end, he sketches out a vision that is very close to my own: a combination of both the unstructured flow of atomic notes and the more curated publishing of their distilled essence:
Still missing from the overall personal knowledge and note taking space is a more tightly integrated version of both a garden and a stream (in Mike Caulfield’s excellent framing) that easily allows interaction between the two arenas. Some of the more blog-based sites with notes, bookmarks, articles and IndieWeb friendly building blocks like Webmention, feeds (RSS, JSON Feed, h-feed), Micropub, and Microsub integrations may come the closest to this ideal.