Another vote for Calibre here. There is a bit of a learning curve to do the more advanced stuff, but nothing a little forum reading won't get one through. Plus calibre lets you convert formats, drop DRM BS with the appropriate plug-ins (I have zero tolerance for copyright protection that in essence often makes it impossible to use books as they were intended to be used, and damned if I'm paying for multiple file formats of the same book that I've already paid for to use on my own ereader.), and perform all sorts of general library management.
I'd even like the idea of a standalone device that performs the functions of calibre with a built-in HD and USB expansion, or at least an android version for my tablet... Hint, Hint, Calibre Developers.