Thank you for the suggestions, =X= and Soilwork.
I would implement several of the suggestions and bug fixes in the next version,
e.g. a crop box that applies to all windows, pretrim option, font-size dependent processing (The last one is very difficult for me to implement - Currently all the processing is done at a pixel-level, not using any PDF informations such as font-sizes, PDF crop boxes, and so on.)
I will also open the source codes based on the free GPL license. (Actually, this is mandatory having used some GPL libraries.)
At the moment, supporting ebook formats is not what I want to spend much time on. (simply because I started this project for my own needs, and I don't need such a functionality.) Sorry.