I like to take notes on paper however my notes are always messy. I'm not able to take notes on anything without having to go back and reorganise them, make sense of them, and add to them. Paper and pen (pencil in my case) are limited in this respect. I'd love to be able to take notes perfectly the first time but find I'll take notes and rewrite them in text (currently zim-wiki) which for me reinforces them in my mind. I can then add/change them when needed. My notes evolve over time, which means paper notes would have to be rewritten continuously with the same information with additions/deletions/expansions/etc. This is much easier electronically, especially when you version your notes (I do this with fossil in zim-wiki).

I find also pen and paper to be limited for programming notes.