Pen and paper, there is something about writing and quickly drawing diagrams using the pen that seems to be involving the right parts of my brain that seem to be asleep otherwise.

Agreed. Pen and paper is great for taking notes

Yet discoverability becomes a huge challenge. I find that I almost never go back to reference those paper notes. I'd need a good system to keep those notes organized

The solution for me is to keep an index in the front or back of the notebook. Each time I write something of significance I put it in the index.

I have something resembling a Zettelkasten using Tiddlywiki with the Stroll plugin. I'm loving it. I feel like this system is taking me from being someone who hoards notes and never looks at them to someone who actively learns and remembers by making connections between newly-added notes and pre-existing ones in my Tiddlywiki.

https://tiddlywiki.com

https://giffmex.org/stroll/stroll.html

Take a look at Emvi [1]. We wrote about how you can use it as a Zettelkasten [2] even it's not build primarily for that.

[1] https://emvi.com/

[2] https://emvi.com/blog/luhmanns-zettelkasten-a-productivity-t...

I'm using Evernote as my main note taking tool. They've put more effort into making it easier to put notes into it than the other systems I've seen and the PARA system was designed by a guy who used Evernote so it works really well with it.

However, I'm starting to experiment with Roam to write more long form notes to see if I can take advantage of the easy linking capabilities it offers

org-roam

Obsidian recently came up here.

Roam Research

great but expensive.