Genius is currently building a tool to achieve exactly this. It's in beta as we speak, just put genius.com/ before any article URL to see an annotated version of it. For eaxmple, here's an annotated version of a "Eloquent Javascript" chapter [1]. If you want beta access get an account and shoot me a message there [2].

We* have been annotating tech articles/papers for a while though, they were stored in a sub-sub-channel of Rap Genius though and didn't get as much exposure. The best example is teh analysis of NewsWeek's story "The Face Behind Bitcoin" [3].

[1] http://genius.com/eloquentjavascript.net/05_higher_order.htm...

[2] http://genius.com/fanahova

[3] http://genius.com/Leah-mcgrath-goodman-the-face-behind-bitco...

*I don't work at Genius, but I've been an editor/mod/intern for the past 2-3 years working on various things including Tech Genius.