I keep notes in text files in sublime. If I want to search, I just do a text search. I generally have many, many tabs (don't the old folks call them text buffers?) open, and when I go through a weekly cleanup of these I find that they fall into two categories:
Stuff that was just, say, a couple of lines of code or urls,
short todo lists that have been todone,
long lists of credentials,
research.
I delete the stuff I don't think I'll need and store the rest in an encrypted store on my main machine.
To your question, these things are things I almost never want to share with folks, my sketches / doodles /etc are generally ephemeral on purpose, and my images are usually parts of projects or collections of similar media, not part of my "notes", and code, of course, is very good in plain text.
Keep in mind that there are reasons why people, myself included, still take notes on pen and paper. For me, it's a single function thing that keeps me focused on the people I am meeting with... I've never gotten a distracting email on my spiral full of graph paper.
So here's an issue you can solve: I totally don't think that there is an "upgrade" for pen and paper in the situations that I use it.
I sometimes have a yearning for a text program like emacs or sublime that can handle images, formulas or other graphical material as easily as paper or onenote. That way I could keep these things together. Not enough that I can't just dump that stuff into a folder, but enough that I find occasional friction.
And though I've never gotten a distracting email on paper, I find it quite easy to do distracting things like doodle, plan dinner, read previous notes, daydream, etc.
EDIT: As I'm brainstorming this, I can see linking to images on the filesystem using a markdown like syntax, then having those images appear when reviewing the notes. Perhaps quickly switching to a program for drawing or automatically syncing pictures of my paper notes or drawings to my PC so I can quickly link those files into the document I am working on.
Since you mentioned emacs, org-mode has the ability to attach files and show image files within the buffer, and it handles previewing latex formulas too.
The problem with these kind of system is that you always need the emacs open, because opening emacs and find the org file you want is too much a friction comparing to opening up a note book and start writing/doodling.
Stuff that was just, say, a couple of lines of code or urls, short todo lists that have been todone, long lists of credentials, research.
I delete the stuff I don't think I'll need and store the rest in an encrypted store on my main machine.
To your question, these things are things I almost never want to share with folks, my sketches / doodles /etc are generally ephemeral on purpose, and my images are usually parts of projects or collections of similar media, not part of my "notes", and code, of course, is very good in plain text.
Keep in mind that there are reasons why people, myself included, still take notes on pen and paper. For me, it's a single function thing that keeps me focused on the people I am meeting with... I've never gotten a distracting email on my spiral full of graph paper.
So here's an issue you can solve: I totally don't think that there is an "upgrade" for pen and paper in the situations that I use it.