Windows\Mac\Linux: If you've got a virtual pile of e-books but no good way to organise them, Calibre is a feature rich e-book manager, complete with Cover Flow-like looks and network sharing. Whether or not you have a portable e-book reader, Calibre is packed with features to help you organise your e-books. To start, you simply tell Calibre where you store your book files. It does a pretty good job pulling the necessary information and self-populating, although you'll still find yourself making occasional edits, like swapping the author and title fields. If you're a LibraryThing user, you can also hook into that account to populate the fields.
Calibre has a Cover Flow-like browsing feature for skimming through the covers of your books. You can leave comments on your reads, and a tagging system for organizing your collection beyond the basics of genre and author. Calibre supports extensive file conversions, with the ability to convert over thirteen document formats into EPUB, PRF and MOBI formats for use on popular e-book readers like the SONY PRS 500/505/700, Cybook Gen 3, Amazon Kindle (1 and 2) and the iPhone (with the stanza reader software). You can also set up Calibre to fetch news from websites and RSS feeds and convert it into a compatible format, so you can load up your e-book reader with information from your favourite sites. There's even a built-in web server so you can access your e-book collection remotely. Calibre is freeware and is available for Windows, Mac OS X, and Linux.