My personal preference is
BookCreator
Basically it is a bunch of Macros for Word. You open the template, import your file and then use MS Word to format it. You then convert it to a format of your choice (you also have the option of adding a cover).
Once I have my file I then import to Calibre.
Personally I have found that the results look a little better than Calibre and you also have more control over what the formatting look like.
Each to their own though...