I am beginning to use a zettelkasten. I think it's an excellent method for doing deep thinking, especially over a long period of time. See https://www.seanlawson.net/2018/02/use-zettelkasten-method-s... and https://zoia.org/2018/11/13/zettelkasten/ for good introductions.

Reading this will change your life: https://www.amazon.com/How-Take-Smart-Notes-Nonfiction/dp/15...

I'm committed to text-only information. No matter how many notes I'm writing, I can always use grep or write my own programs to find what I want.

If you're on a Mac, The Archive is great (https://zettelkasten.de/the-archive/). It's what I'm using

zettelkasten.de has lots of good reading (thanks, Sascha and Christian!), but look to the other sources I've listed to get a more thorough idea of what a zettelkasten is (I call mine a thinking-box) and how to use one.