It's funny, but I can't do most of those things (keep trying to emulat @devonzuegel's Evernote use, with no success). In fact, I'm moving mostly back to paper, to Anki, and to pinboard. So much easier (for me).
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I miss really good hyperlinking on paper (though I do add pointers occasionally when they occur to me... they're super-easy to add, but do take a few extra seconds to follow). I wish I could do auto-machine-generated hyperlinks on paper...
Really want a Remembrance Agent for paper: http://alumni.media.mit.edu/~rhodes/Papers/remembrance.html … (Emacs plugin that automatically found context for whatever you were writing).
