I usually read my books using an application called Mantano on Android. They have a cloud based sync mechanism that syncs annotations across various mobile devices.
My problem is I want to keep all my books in Dropbox (or maybe Calibre) and want to keep all the annotations, bookmarks in one place (preferably within the book itself) so that if in future I want to change the reading software on any platform, I have the annotations right there.
Is there any solution for this? I mainly read epub and pdf books. A single reader is the best option but if not possible I can use two readers (one for pdf and another for epub). I want to stay away from dedicated readers like kindle, nook etc.