Amazon Digital Books uses its proprietary format called MOBI (also called Kindle format), while Apple uses an open format called ePub

Amazon and book publishers' stupid attempts to curtail e-book lending.

Imagine a future where instead of lending someone a book, you lend them your bookmarks. Where your notes, annotations and references are synchronised across platforms and applications. Where your bookmarks belong to you, and a record of every book you read is saved and stored securely, no matter how or where you read it. We're nearly there, and that's why we need Open Bookmarks.

Ephemera will comfortably synchronize your ebook reader with Instapaper.com via USB. It works with the Amazon Kindle, Sony readers and pretty much any device capable of reading HTML, Mobipocket or EPUB files.