If you’re looking for a one stop solution for organizing your eBooks, backing up and syncing them to Dropbox, and reading and annotating them, KooBits is a free Adobe AIR-based solution.
KooBits is a combination eBook organizer, reader, synchronizer, and even bookstore (you can purchase books in the KooBits store, but it’s not necessary to do so to benefit from all the features in KooBits). Many eBook tools either open eBooks or organize/display eBooks, so KooBits is a nice departure from the either/or situation you often find. You can read your books, annotate them with a variety of marking tools, sync them to your Dropbox account, and more. Check out the video below to see it in action.
KooBits is a free download and works wherever Adobe AIR does.