My notetaking is completely influenced by having jumped wholeheartedly into TheBrain 25+ years ago. (I was the first analyst on their first press tour.)

Using TheBrain I can connect notes not only to the works I found them in, but also to the broader ideas that hold them, which then makes them neighbors to related works.

You can see an example from my notes here: https://bra.in/8p6WdQ