We are working on HTML5 annotation support, which will behave very much like our Silverlight WebViewer's support for annotations:
http://www.pdftron.com/silverdox/samples/ReaderControlSample.html
The HTML5 Viewer will have a similar API, and the resulting annotations data (stored in xml) should be interchangeable between the HTML5, Silverlight, and Flash viewers.
You can see a developer's preview of the HTML5 annotations viewer here: