If I'm looking for something recent or that I already know the approximate date the note was made on, I just read through the notes from the relevant time period. I also keep notes in my physical notebooks about what information is found in which note textfile on the computer.

In practice, I rarely actually need to grep or otherwise use tools to search through the notes. My eyes work fine (and, for me, are even better because I get reminded of the context in which the notes were taken).

The odd thing about the paper notebooks is that I rarely actually need to use them. Just the act of making the notes greatly enhances my natural recall of them anyway. If the notes are something deeply technical (a bunch of raw data, schematics, whatever), having written them by hand also makes me remember where I wrote them. That sort of thing only happens when handwriting, though (which is why I came back to handwriting notes). It doesn't happen at all if I've typed them into a computer.

I've probably tried just about every "knowledge manager" or note-taking application there is at one time or another, but for me and how my brain works, nothing comes close to being as effective as writing things in notebooks.