Reddit mentions of Practical Cryptography

I followed the rabbit-hole a bit, and landed at this book: https://www.amazon.com/Practical-Cryptography-Niels-Ferguson/dp/0471223573/

In which "double SHA-256" is discussed as a way to prevent attacks on SHA-256 from affecting your hashing algorithm. There's a known advantage to running multiple rounds of a hashing or encrypting algorithm (see bcrypt which is recommended for multi-round hashing of passwords for storage in a database).

wow... r/java is probably not the place for this, you should be in r/crypto. crypto is a big and in depth field, expect a very long learning path. Taking this and reading this will give you a start. For java, try bouncycastle and his book. We regular folk are not advised to write algorithms or protocols.

To add to this: Practical Cryptography by Schneier and Ferguson is my top recommendation.

Everything you ever wanted to know about cryptography (but not necessarily all cryptographic algorithms) is in Practical Cryptography. If that doesn't fill your cup, then put on your big-boy pants and dive into Applied Cryptography. You will note that Brian Schneier is a common author between those two books. There is a reason for that. :-)

I started with this book: https://www.amazon.com/Practical-Cryptography-Niels-Ferguson/dp/0471223573 and can't recommend it strongly enough as an entry point.

It doesn't get into the algorithms but instead the different types and modes of encryption, when you would want to use them, and why. That can serve as a nice jumping off point to more detailed research.

It's a very approachable book and you'll come out of the book knowing how to use crypto well.

I highly recomment Practical Cryptography - I heard there's a newer version out from the author but I haven't read that one personally, it's probably worth checking into. It's a great book for beginners, it goes over mostly methodologies and implementation, a bit of the math too.

Bruce Schnier and some other guy's Practical Cryptography

The ever-excellent Khan Academy has produced a very nice and short series of videos explaining how cryptography works. Anyone who understands basic high school arithmetic can follow this. If you have ever been interested in the science of codes, ciphers, breaking them, etc. this is worth a look:

http://www.khanacademy.org/science/brit-cruise/cryptography

More in-depth treatments of cryptography can be found here:

https://www.coursera.org/course/crypto

and here:

http://www.youtube.com/playlist?list=PL71FE85723FD414D7&feature=plcp

And for the truly hard-core some of best books on crypto are:

http://www.amazon.com/Applied-Cryptography-Protocols-Algorithms-Edition/dp/0471117099/ref=sr_1_1?s=books&ie=UTF8&qid=1340524661&sr=1-1&keywords=applied+cryptography

and

http://www.amazon.com/Practical-Cryptography-Niels-Ferguson/dp/0471223573/ref=sr_1_1?s=books&ie=UTF8&qid=1340524712&sr=1-1&keywords=practical+cryptography

and

http://www.amazon.com/Cryptography-Engineering-Principles-Practical-Applications/dp/0470474246/ref=sr_1_2?s=books&ie=UTF8&qid=1340524751&sr=1-2&keywords=practical+cryptography