I can't see Apple and Amazon working together. Apple tends to want to dominate the entire supply-chain and I think that only works when they're dealing with comparatively unsavy companies. Amazon gets the web well enough that they're not going to hand over control to Apple wholesale and I think that'd be a deal-breaker for Apple.
I can see them taking the publishing side end-to-end. Add stuff to Pages to simplify publishing a book -- all aspects, cover to cover. Become a middleman for offering indexing services. Have an online publishing service that automatically translates your file as an eBook, lets you order ego copes, and also enables bookstores to order it as product.
I know there are services out there, but the physical product is a bit shaky, and they don't have slick software integration with the service. Apple is in a great position for that kind of integration.
