Hey Everyone,
ReadSocial just released two open source client libraries for annotating ebooks on the iPad and on the web. Thought some developers here might be interested in looking at the github repository or the API documentation.
Details at
http://www.readsocial.net
Quick explanation: Integrating the code creates an overlay on HTML or iOS reading systems to create groups and paragraph-level comments (which can be images, text and links). Changing the group changes the note overlay. Disclosure - I'm part of the team.
Thanks,
Travis