Note Taking Challenges: Physical

Good notes are useful, but it is difficult to determine what good note taking looks like. What constitutes a good note is rather personal and contextual to the task that the notes are being used to solve.
As time goes by, old notes become hard to find, and even harder to determine whether it was worth the time to make them.
As a knowledge base grows, organization feels impossible, finding things is difficult, and the discoverability of even the simplest of ideas feel like a lost cause.
Once a knowledge base becomes large enough, it becomes easy to question the value of continuing to take notes. How do you measure the value you've gotten relative to the effort you've invested?
Trying to organize by categories first consistently fails in the long term, since it requires upfront definition of a body of work that does not yet exist. Over time, hierarchy fails to adequately fit and reflect it's content.