With pen and paper. I prefer paper notes that just look like Zettels by Luhman. I strongly believe using a pen and abstracting what I read into my own thoughts improves my notes. I do include citations, but most of the text is my thoughts of what I read.
Afterwards I have to type the notes from the paper into my DT. This feels double work to many others, but I feel it is necessary. Sometimes at this point I just don’t put my original note into DT at all (and just delete it by destroying the paper note). This also means my reading sometimes needs to wait on my writing, for if I have too many paper notes waiting to be put into my laptop, I just dread them and don’t do anything. At this point, my reading then must switch to reading with no notes (which means mostly novels).
My only digital reading is in the browser. Articles from there get clipped into a subfolder of my “source notes” folder, because mostly I just tag them and do no abstract. If I do an abstract of a web article, I put it in front of the markdown clipping of that article and such a summarized web article goes into my “source notes” folder.
The rest of my reading is on paper: academic papers I read on paper and put the notes in the margins, later using these notes to summarize the paper. Some of this stuff also lands in their own “content notes/zettels”. And when I read books, I always read them on paper and carry around with me some paper notes.
Here a photo of such a paper note and the paper Zettels I use and in the background you also see my paper notebook, which I carry around for putting down notes everywhere: