I came across a very simple and practical organization system called the Johnny Decimal System. Apparently, this is proposed by Johnny Noble. I'm amused (or is this really the name?).
My knowledge organization is partly inspired by this. I summarize some key points below.
Everything is organized into areas and categories. It is a two-level organization system where it is advised to not have too many of them.
IDs are assigned as serial decimal numbers from 00-99. There's no pre-defined order attached to these numbers and semantics are defined on the go as needed. While nothing stops us from going beyond 99, at this point, one may have over-organized and should split up an area.
Using this organization on a file system, nothing is ever more than two levels deep.
It allows exceptions to all the rules, which aren't many in the first place. It's pragmatic and I like it!