I am a massive fan of evernote, it's one of those applications that I can't do without. I type all my notes into it, scan everything into the application, I basically have it open all of the time.
I like to ensure that every note is filed into the relvant notebooks and more importantly that every note is tagged. Occasionly I will file a note a way without tagging it, and then trying to find them again is a pain. However there is a very simple way...