Calibre is the best management software you'll find: it allows conversion between all sorts of formats, supports plugins for stripping odious restrictions, can transfer to hardware devices, and, while the UI is rather clunky, it does just about all you'd need for ebooks.

I'm not sure from a reader perspective: you'd want one that can be jailbroken, and that's just not something I've looked into. I live with the Kindle's firmware.