I use plain text files for notes that don't require major formatting and figures (e.g., notes on programming, sysadmin, food recipes, etc.). To find something later, I simply grep -iR <word> inside the notes directory.

I also make notes involving equations and figures, and for that I first make draft versions of the notes on letter-sized unruled paper using a fountain pen, and then LaTeX them up when I think that they're worth typing up. I almost never LaTeX notes without making draft notes first. Sometimes I also use my office's scanner to scan my handwritten notes.

I also have a Pinboard account for bookmarks.