Comment by pantulis

This is it. The key aspect for any productivity or "second brain" tool is the overarching taxonomy. Wheter you use Johnny.Decimal or Zettelkasten or whatever the trend is, you need to sit, think this stuff hard enough, configure the same exact taxonomy in your weapons of choice (say Evernote, Omnifocus, Gmail) and then stick, stick, stick to it. Also remember to review it from time to time, is it working as expected?

Otherwise you end up with a digital ball of mud, and you can only extract info from your system using the search. Maybe this works for you, maybe not.

I like that Johnny.Decimal assigns memorable ids to the categories, this is absolutely nice and is easy to follow by members of a team.