My recent findings is that it's better to not take any notes at all. Instead of adding some item to your todo list, do it immediately and don't send it off like some nasty surprise to your future self. The smaller my notes.txt the less complications I have to worry about and I can go on living a happy and fulfilled life.
Currently I'm designing a large VR environment for a game. Without notes of what needs to go where and when, that would be going... less well.