I am familiar with John the Ripper, nevertheless, I haven't found a source where I can familiarize myself with the theory behind the program. I know that by studying the code I can get to understand how it works, yet I would like to read something where the techinques used by the program are studied in deep. Can anybody give some suggestions? Just to get it straight: I would like somebody to point out a reference where I can find the "theory" behind password cracking. Thanks.
Have you checked out Openwall's publications? They have published articles and presentations with some good material.
Also here is a nice paper that discusses some of the different methods and how they work.