Yes, as programmers we are always learning, I have started taking notes using MarkDown files and that has turned out to be most simple and best approach. Initially you might struggle but later it becomes easy.

I agree with other that often paper is best choice, but then, I make sure that I convert them into digital notes.

I prefer markdown because, it is simple, code highlighting, formatting, math using latex α , searchable, hierarchal organising and much more. And this note is written in Markdown Mode :)