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. www.ciphersbyritter.com/JAVASCRP/NONLMEAS.HTM
Chaffing and Winnowing - An interesting paper by Ron Rivest about providing confidentiality without encryption. theory.lcs.mit.edu/~rivest/chaffing.txt
Foundations of Cryptography - Oded Goldreich. A public domain book available on-line. Only partially completed. theory.lcs.mit.edu/~oded/frag.html
Hasanov's Articles - An introduction to the use of prime numbers in cryptosystems and to the analysis of weaknesses of algorithms. hasanov.ilm.uz/articlese.htm
Index of Cryptography Papers Available Online - A research tool for the cryptography community maintained by Counterpane Systems. Over 400 papers online. www.counterpane.com/biblio