I've been wanting to try out some web-based annotation tools for use in peer-review and collaboration, so I've installed a copy of Geof Glass' very cool Marginalia and imported an example document into it (with the author's permission) - feel free to add and edit annnotations (though please don't delete other people's annotations that might be useful). There's also a test page that doesn't store annotations, with some instructions.
Marginalia is really well made: it's all Javascript and PHP, with MySQL storage and all the communication done using Atom (which means you get an Atom feed of recent annotations for free).
It's very basic at the moment as there's no user control, so anyone can deface the annotations. What I'd like to see eventually is a wiki-like editing interface for the main content (with the ability to fork off new versions) and non-anonymous annotations, as well as voting by reviewers (+1, -1, abstain) on whether to accept an article for publication.