I have to plug Hypothes.is [1] who are doing this in an open source and distributed fashion. They have quite a team and a lot of grant money to make it happen.
Hey whoever's building this -- please give me a shout. christianpbrink at gmail. If you haven't built it yet, maybe you don't need to, as I already have and may be interested in a partnership.
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[ 2.9 ms ] story [ 22.5 ms ] thread[1] http://hypothes.is/
What would be most interesting out of all this is a viable open annotation protocol, and an infinite number of federated sites that use it.