Originally Posted by cypresstwist
I read somewhere yesterday that if you make annotations in a book using your Nook, that particular book should display those annotations in other EPUB reading software. This means that the annotations should be stored within the EPUB file itself.
This is a goal of epub 3, the next revision of the standard, but it is not in the current spec (see here
for the draft implementation). If any existing epubs try and do this it is at best a draft implementation, and probably just proprietary.