Updated to version 1.1. Added color support and you can specify number of colors. So now this can be used to prepare manga for the iPad.
Also, I got tired of calling this "my manga processing program" so I gave it a name: Canti, after the Medical Mechanica robot from FLCL. If you don't know what I'm talking about, don't worry about it... it's from a manga so I thought it was appropriate.
You'll notice the "KDX" in the filename. That is because the .properties file is already tailored to the Kindle DX. I'm going to post the program in the iPad forum with the .properties file customized for them.
Anyway enjoy and let me know if it works for you
Oops, in adding color support I accidentally broke grayscale. I've removed the download link for v1.1. Download the latest version below instead.