The Paragon Initiative has posted an article about cryptography, introducing some of the basic concepts and explaining why "you wouldn't base64 a password" to adequately protect it in your application.

If you feel that cryptography is a weird, complicated, and slightly intimidating subject for which your feelings might be best described as lukewarm (on a good day), we hope that by the time you finish reading this page, you will have a clear understanding of the terms and concepts people use when this topic comes up.

He starts with some of the basics around hashing (keyless cryptography) and the advantages/disadvantages of the method. He moves from there a step up and gets into secret key cryptography, using things like HMAC hashing to ensure message validity. The next move up is to secret key encryption, using some kind of "secret" as a part of the encryption process along with the right algorithm and mode for the encryption level desired. He also covers authenticated key encryption, public key encryption, shared secrets and digital signatures. He ends the post covering some of the common pitfalls of using cryptography in things like password storage, file verification and a reminder that encoding (like base64 encoding) and compression aren't encryption.