+1 for "use search instead of organization".

I've been taking notes for 2 years, zettelkasten-style, and 90% of them are just dumped in the same directory, without links or tags. If I'm looking for something and remember that I might have that in my notes, I just search for it.

That also implies that, when writing a note, I sometimes add a line with a few related keywords and synonyms.