Since getting my Kindle I've amassed more and more eBooks and one of the best tools I've found to manage all these books in Calibre. This is a free and open-source tool that helps you manage your library of eBooks and best of all it's available to Windows, Mac and Linux users.
Calibre is rather like iTunes for your eBook, it allows you to define metadata for your books such as tags that allow you later to search for books. Alongside helping you to manage your collection calibre also allows you to convert books to different formats such as PDF to MOBI. Although the Kindle does support PDF I tend to prefer converting the PDF to MOBI before dropping it onto my kindle. All of which is very easily achieved using Calibre.
If you have any eBooks I highly recommend that you check out Calibre. More information and the latest version can be obtained from: http://calibre-ebook.com