I use Calibre and it works great with my Kindle 3G. It needs very regular updates (very regular!) and the "recipes" are still a bit of a mystery to me. But as a free, featured app, it does what it sets out to do very well.
Does anyone here use Calibre to organize their ebook library? I'm thinking of using the portable version of Calibre to manage my Kindle Touch via my Dropbox account.