For those who might be looking for a desktop application, Calibre http://calibre-ebook.com/ is an awesome FOSS ebook manager. Organizes, converts between formats, etc.
As a recent owner of a Sony e-reader, Calibre is really functional, but I don't think I've ever seen a worse interface.
While Calibre is a brilliant application for basic document management and conversion it should be mentioned that it is highly unlikely that it will convert a PDF eBook perfectly. I've got a bunch of free CS books I've collected over the years and outside of plain-text books it's struggled to convert everything.