I believe writing notes is essential for scientific research. Both for future reference, and also to provide space to think.
I develop a lot of my understanding on paper. Once I’ve read and thought a bit about a topic, I really like starting with a fresh A4 page (or double spread) and writing down pointers to everything I know about the subject, little diagrams and snippets of mathematics. This would be wholly useless for anyone else to consult, but I find makes a good jumping off place for my thoughts, and something I can return to and rework.
For meetings and conferences I have come to the conclusion that a laptop or tablet is a mere distraction, and all I need is a physical notebook. I believe that physically writing helps me remember. If I do nothing during a seminar, I find myself day-dreaming or outright snoozing.
Organising physical notes is a pain, always. I think the least-worst option is to keep everything in one book, with every meeting dated. Subject-specific notebooks always seem to end up in the wrong place at the wrong time (i.e. at home / work, on my desk rather than with me in a meeting). That said, specific notebooks for lecture courses or conferences seems to work well. Leaving blank pages, to e.g. finish up mathematics, never seems to end well. I also find explicitly writing who else was present at the meeting, and physically where it was, helps me remember what was going on when I refer back. I find flicking through my notebooks even if not reading them properly help refresh my memory.
Of course, a lot of my work is on the computer. Typing is the natural place to start developing conference abstracts / papers / applications. For this I’ve been using [https://simplenote.com] since the start of 2018. It’s a very lightweight text-only note taking website / online app. The phone sync means I can always refer to everything I’ve written. I started it off by copy+pasting in similar things I’d had stashed in my Gmail inbox + [https://draftin.com] + ~/NOTES folder.
The interface to Simplenote is very bare - with a (reverse modified date sorted) list of notes in the left column, with the first line of the note as title, and second line as small-text subtitle. I now prepend all my notes with REVIEW/LEARN/PAPER/JOB/ABSTRACT etc. to identify what is going on.
The boundary between the computer and the physical is a challenge. I think
people who start obsessively indexing / scanning their notes are wasting effort
on something which isn’t actually a problem.
For a bare minimum of cross-referencing, I label my notebooks (20XX.Z, where
Z is alphabetic for an A4 work-notebook, and numeric for an A5
meeting-notebook), and number the pages. When I have spare time I fill in the
‘contents’ first page, and write some info on the cover.
So I sometimes end up with ‘see yellow
notebook 2017.3 p.24’ in code/latex comments.
I regularly find myself writing long-hand references to data / files, usually in a similar manner to my command prompt: ‘machine:~/WORK/2018-project/blah/fixed-blah/reallyfixed/’ etc.
Physically I use Clairefontaine Europa Notemakers, which have a really nice smooth paper. I generally write with a Pilot G-Tec-C4 (0.4 mm fine rollerball), though the 0.3 mm version (often sold in a slightly more bulky Maica plastic body) is better for mathematics + marking up papers.