.jar is indeed a Java Archive - some books have been packaged up so as to be readable on a mobile phone. The .jar contains effectively the reader and the book.
I would think most books of this sort could be sourced in a "proper" format rather than messing about trying to de-construct the packaging of the .jar.
Gutenberg have a Qioo format that is somewhat similar. I have unzipped a Qioo.jar archive and it contains amongst other things a text file called "data" which is the book in simple text format. As the text contains the usual Gutenberg headers it would be much easier to download the original text !