I have been using Keynote [1] for years, without ever losing information. I find that its tree data structure is extremely useful. It is an open-source desktop program. Unfortunately its development seems to have been put on hold. It would be great if developers would keep it updated (on Windows 8, there are some small UX glitches).
[1] http://en.wikipedia.org/wiki/Keynote_(notetaking_software)