Nope, first I've heard of hypothesis! However I have seen a few things like it/Epiverse (Genius is doing something very similar to hypothesis). Apparently during the conception of the internet web annotations were planned as a feature. I think we're still a way off web annotations (very ambitious), but a good bridge is a comments system, which I think we are ready for.
Thanks for the suggestion! I'll look into it. I am wary of asking permission from host sites because then it's not necessarily user controlled (plus there wouldn't be a huge difference between us and something like Disqus). There are potentially ways I could integrate things like host verification for comments though.