I wish HTML were more readable. If we have to design it now, probably it would be more of wiki-markup-like more readable without the ugly angle brackets. For this reason, it is not suitable for casual note taking.
I take notes in plain text. I configure my vim editor to highlight the texts like Note: Todo: and some more of my own syntax rules for the .txt filetype just so that it looks nice when I read them. However just cross-referencing different sections within and across documents is not as smooth as I wished.
Here comes -- Markdown and RestructuredText markup languages-- you take notes which is completely readable in text form, and yet convert to HTML/PDF/other formats later for better consumption. I have now adapted Markdown and RestructuredText as my primary means of taking notes.
Markdown is also the primary markup language used in stackoverflow and github, so it helps to be familiar with this stuff.
Hope it is useful as quick reference for those who are interested.