Here’s the setup. O’Reilly hosts a django based open source ebook reading website called bookworm.  You can run bookworm on your own server.  I opened a ticket on bookworm’s bugtracker to provide an api method to update where you are in a book.  Next you update Aldiko (Not open source, but perhaps we can write a plugin for it) and FbreaderJ to use that method when they exit to update where you stopped reading.
Upshot: You open a book on your phone and read it. Â It syncs with your server with a bookmark of where you stopped reading. Â Then you go to your website, and begin reading from where you left off. Â And so on. Perhaps your phone also detects when it gets a new ebook and uploads that to your server or downloads a new book from your server when one shows up as well.
