I do most of work in Emacs and use various notes files which I edit in org-mode. For example I have general 'personal.org' and 'research.org'. Then, on projects I work on I usually have misc .org files under 'doc/' directory. Such as, 'ideas.org', 'todo.org', etc. They are easy to edit in emacs with formatting and collapsing levels, and yet are readable with 'less' or could be even edited with 'vi' if I ssh somewhere.