In my research I take notes exactly as described here. I use plain-text files, one per week, with dated sections using markdown-ish notation where convenient. Display is never a goal; approximately 80-char column plaintext is the target format.

I agree with other commenters here that typing gives me more flexibility, in particular when writing arguments. I’ll format each point as a bullet and rearrange the list until I’m satisfied with the flow.

The notebook is essential for recovering tidbits learned along the way, e.g. what tricky steps did I need to get that one dependency to build. Weekly notepads are coarse enough to search by memory and contain enough context to get oriented quickly when going back several months.