All my various notes these days go into one large org file that's turned into a fun little model of entropy.
The doc is thousands of lines long at this point, and as ideas get more organized they tend to move up the page into increasingly formal, structured trees. Towards the bottom are more half-thoughts and temporary todos that have yet to be developed and find their place.
@devlaf this is me except i never clean them up
also all my bash scripts are code blocks in a giant org file now