I have yet to buy any ebooks from amazon, just downloaded most of mine through "3rd parties", and the kindle is a wonderful device for that, thus I can share my books with whoever I like.
Wish it would also sync the non-Amazon books, though. Maybe I am not proficient enough yet, but so far I had to copy ebooks into obscure directories by hand (especially interesting on the Android Kindle reader).
Or setup a spideroak sync folder for the ebook-folder on your android, and just sync your non-amazon books through spideroak.