Based in the S3 Cloud (of course).
Every book has a unique Wiki based on ISBN.
You annotate via a Kindle-browser-friendly blogging engine.
You can view threads chronologically (normal blog view) or if they incorporate references to Kindle "positions," they can be threaded by location in the book.
Server-side stuff is easy enough; Kindle-friendly blogging editor/display reasonable; barrier to entry is difficulty getting from Kindle reading to Kindle browser (Home -> Experimental -> Web -> Bookmark). Also, positional permalink should be easy but will be hard ("Remember your position in the Kindle book" H->E->W->B -> Note Editor, add text, enter position in field).
Also, links ought to be two-way ("Read Now" ought to open that page in Kindle), but impossible with current firmware:
