[Adoby]

Here is a minimal script to do the job. Written for bash. Tested in Ubuntu 13.04 with calibre 0.9.38.

Assumptions:

• The original epub books are all in the folder ./books when the script is started. No other files are there, except the epub books.
• Names of all fonts are in the file ./fonts.txt. One line per font name.
• The fonts are installed in your system.
• The original books are all in good shape and no fonts are embedded in them.
• You will most likely wish to add more options to the ebook-convert command.

You can have as many fonts and books as you like.

The script will create a output directory ./books-FontName for each font and store copies of all the converted books, with the same name as the original books, with the font embedded as the base font.

Sample fonts.txt:

Liberation Serif
Bitstream Charter
DejaVu Serif
FreeSerif

The script:

#!/bin/bash
cat fonts.txt | while read FONT     # loop over font names in fonts.txt
do
   mkdir """books-$FONT"""          # create output direcory
   cd """books-$FONT"""             # and make it current
   for BOOK in ../books/*           # loop over the books
   do
      ebook-convert """$BOOK""" .epub --embed-font-family """$FONT"""
   done
   cd ..
done

I believe free/opensource versions of bash are available to install and run in Windows. I have not tested to see if the script works in Windows.