This freeware application is the ultimate eBook library manager. Use this application to catalogue your extensive eBook collection (featuring support for similarly extensive metadata). From there, you can convert your files to a variety of supported formats, depending on which reader you're using to actually view your eBooks. And don't worry, you can use Calibre to synchronize your information and files straight to your device. Take that, extraneous applications. Oh, and did we mention that Calibre can convert RSS feeds into "eBooks," perfect for reading your day's news without the need for an Internet connection.
Thanks to Karamjit Lal for the update.