Theory

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.

Index of Cryptography Papers Available Online - - A research tool for the cryptography community maintained by Bruce Schneier. 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.