Foundations of Cryptography
- Oded Goldreich. Focuses on the basic mathematical tools needed for cryptographic design: computational difficulty (one-way functions), pseudorandomness and zero-knowledge proofs.
- http://theory.lcs.mit.edu/~oded/frag.html

RSA Security's Official Guide to Cryptography
- Burnett and Paine. Explains the differences between symmetric-key and public-key cryptography, how PKI and X.509 affect security and how the RSA algorithm works within protocols.
- http://books.mcgraw-hill.com/getbook.php?isbn=007213139X

Handbook of Applied Cryptography
- The online version of the 1996 CRC book by Menezes, van Oorschot and Vanstone (5th edition) in PostScript and PDF formats.
- http://www.cacr.math.uwaterloo.ca/hac/

Cryptography Decrypted
- Mel and Baker, has sample chapters.
- http://hxmel.com/

The Interactive Cryptography Tutorial
- Online tutorial with useful info and links.
- http://www.antilles.k12.vi.us/math/cryptotut/home.htm

The Code Book
- Simon Singh. Traces the development of codes and code-breaking from military espionage in ancient Greece to modern computer ciphers.
- http://www.simonsingh.net/The_Code_Book.html

Cryptography book recommendations
- Cryptography book reviews, links to online erratas, and free book downloads. Most books have charts that recommend prerequisite books, mathematics and programming language experience.
- http://www.youdzone.com/cryptobooks.html

In Code
- Sarah Flannery's supplement to her book "In Code", describing her Cayley-Purser algorithm.
- http://cryptome.org/flannery-cp.htm

Security Engineering
- Anderson, Ross. Author describes book in his own words. He explains how "pure" cryptography is not quite so pure when expressed in the context of real world applications.
- http://www.cl.cam.ac.uk/~rja14/book.html

Cryptography Theory and Practice
- Douglas Stinson. Subtitled "Discrete Mathematics and Its Applications". Written with more emphasis on theory than practice, as acknowledged in the preface.
- http://www.cacr.math.uwaterloo.ca/~dstinson/CTAP.html

Contemporary Cryptology
- Gustavus J. Simmons. Subtitled "The Science of Information Integrity". Has emphasis on the cryptographic elements of the subject.
- http://www.wiley.com/cda/product/0,,0780353528,00.html

Primality and Cryptography
- Evangelos Kranakis. A comprehensive account of recent algorithms developed in computational number theory and primality testing.
- http://www.wiley.com/cda/product/0,,0471909343,00.html

Cryptography for Visual Basic
- Richard Bondi. Subtitled "A Programmer's Guide to the Microsoft CryptoAPI" which describes what the book is about.
- http://www.cryptovb.com/books/bondi/bondi.html

An Introduction to Cryptography
- Richard A. Mollin. Intended for a one-semester introductory undergraduate course in cryptography. Covers symmetric and public key systems with chapters on advanced topics.
- http://www.math.ucalgary.ca/~ramollin/cryptopref.html

Applied Cryptography
- Bruce Schneier. A comprehensive tutorial and reference but a little light on mathematical theory.
- http://www.counterpane.com/applied.html