In the past notetaking never really was my strongest side. Eventhough I did take notes on paper, quite consistently in lectures and during talks, they always ended up being somewhat hard to read. Digital notes would probably make more sense.
During my PhD I developed a more well thought-out workflow for making notes and writing in general. My Master's supervisor Mathieu Renzo used Emacs a lot so I thought why not give that a try. The extension org-mode made writing notes a lot more pleasant, and provides a wealth of functionality for organising and planning. Big thank you to Carsten Dominik for writing that package, wish I knew about it when I followed his courses at the UvA in Amsterdam!
What really helped organising my notes was Org-roam, and since I picked that up, I have been writing a lot more, trying to build a knowledge-base to help me with my research (along the lines of the Second-Brain ideas).
I will post my dotfiles repo link at some point, it currently is such a mess that it won't be that useful for others.
It took quite some time to get everything set up as I want to, and I'm still changing things quite regularly. It also required diving into Emacs, something that.
Since this is not very beginner friendly I tried to find some alternatives to the (org-)roam based set up that we're more plug-and-play. Obsidian seems to be a nice alternative, it has a good community with lots of plug-ins.