Grrr this is one of my pet peeves with the ePUB standard. Not standardized way of storing annotations.
Moon+ has the ability to export and import notes/annotations/bookmarks that are created from Moon. It is located in the "share" link in the Annotations dialog box. It also has the ability to share all of your notes to a variate of apps, email, tweeter, facebook, evernote, etc....
One thing I've gone to doing is saving all of my annotations/notes to evernote. If ever the case I need to look up something from a book I read. I can search the evernote database. Right now no app has a nice and easy way to search on your apps and evernote is build for such a feature. It also is a great way to backup ones notes. I have lost good notes both on Kindle and Android devices because for a multitude of different reasons.
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