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. It syncs with your server with a bookmark of where you stopped reading. Then you go to your website, and begin reading from where you left off. 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.