My ZKN database is a workshop. Each note acts as a workbench1, preserving progress-- a digital representation of stacks of papers and crafting tools organized on a table. It's a state to which I can return and, at a glance, pick up where I left off-- invaluable if you're someone like me, collecting hobbies at every turn, interested in everything, and invariably short of time.
The Obsidian.md note-taking database has been invaluable, using simple markdown text files but providing tools for trivially interlinking notes, and plugins for an enormous number of custom tasks (including my favorite, Dataview, a query language and display format).
At current count I have over 550 main notes on topics ranging from the Black Plague and the Hieropolis Gate to types of exercise, cuisines, Drupal module development, worldbuilding, and the Traveller campaign I'm playing in-- plus more than 120 work notes, 200 recipes, 1500 bits of fiction, and 2400 daily note files.
Everything goes in the zkn. Organization is organic, evolutionary, and ongoing.
^1: This notion comes primarily from Andy Matuschak's concept of evergreen notes.