I can't comment on Calibre or the Feedbooks editor since I've never used them myself but they seem to get a LOT of publicity on this site. I can say that I've been using BookDesigner for almost 2 years with great success. Do a search in Mobileread for BookDesigner and you'll find a great deal of helpful information on formatting and using the application. It is one of the best e-book tools I've ever come across!
(It seems a lot of people see BD as a daunting piece of software but once you learn the basics you'll not be disappointed.)