I've been contemplating on switching to ebooks, and may setup a central Calibre server in future. One issue I still haven't figured out is that how can each person's notes and annotations should be handled.
As much as the convenience of using a single service like Kindle and Nook provides, I don't like the aspect that books may not be passable from one generation to the next, and sharing between family members is still something to be developed. Moreover, the thought of having your book collection controlled by a corporation which can delete your books anytime it likes doesn't sit well with me.
We need a better way to standardize, store and manage the notes and annotations, so it seems.
Cheers.
Edit: Seems the EPUB working group is working on annotation-related stuffs for the next revision.
http://code.google.com/p/epub-revision/wiki/Annotations