I use both Calibre and Book Designer. For simple conversions, Calibre is definitely the way to go. It's very easy and the program does all the work for your.
Book Designer is what I use when I know a file is going to need a lot of manual formatting. Book Designer is a good program, but does have some quirks and bugs and is beginning to show it's age. (No ePub conversion for example.) As far as I know, there is no one actively supporting Book Designer, so it's unlikely that we'll ever see any updates to it.
dordale