Bibliography on Secret Sharing Schemes: List maintained by Douglas Stinson and Ruizhong Wei.
Boolean Function Nonlinearity: A detailed discussion of cryptographic nonlinearity, what it means and how it is computed, with active JavaScript panels to perform the computation.
Chaffing and Winnowing: An interesting paper by Ron Rivest about providing confidentiality without encryption.
Claude Shannon's Communication Theory of Secrecy Systems: 1949 Bell Labs research paper on theoretical secrecy and perfect encryption cryptography.
Cryptodox: A community wiki. Basic cryptography theory and information security resources.
Foundations of Cryptography: Oded Goldreich. A public domain book available on-line. Only partially completed.
Index of Cryptography Papers Available Online: A research tool for the cryptography community maintained by Counterpane Systems. Over 400 papers online.
Introduction to Cryptography: Elementary information on cryptographic theory, digital signatures, protocols, and cryptanalysis.
Paul Garrett: Crypto and Number Theory: Lecture notes for a course on cryptography and number theory.
Random number generation and RFC 1750: Information regarding best practice random number generation for cryptography.