Lecture notes on cryptography, Shafi Goldwasser, Mihir Bellare
Handbook of Applied Cryptography
A computational introduction to number theory and algebra
Number theory, Z.I. Borevich, I.R. Shafarevich
Introduction to Number Theory, Hua Loo Keng
A course in computational algebraic number theory
Algebraic Number Theory, Serge Lang
Foundations of cryptography, Oded Goldreich (some materials here)
Mathematical cryptology
Cryptography and network security : principles and practice, William Stallings
Princeton's COS433
MIT's 6.857
MIT's 6.897 Selected topics in Cryptography
MIT's 6.805 CryptNum
Luca Trevisan's courses
Vinod's computing on encrypted data course
RIT's CSCI 462
Stanford's Elliptic Curve course
Berkeley's CS174
Regev's lattice course (2004)
http://kodu.ut.ee/\~lipmaa/crypto/
Post quantum crypto, by DJB
SafeCurves: choosing safe elliptic curves
The matasano crypto challenges
Stick figure guide to AES
Cryptography and Number Theory for Digital Cash
Elliptic curve cryptography: a gentle introduction
SEC 1: ECC
sockpuppet.org
A few thoughts on cryptographic engineering, by Matthew Green
Schneier on Security
Matt Blaze's EXHAUSTIVE SEARCH
Security audit of EncFS
Security audit of ecryptfs
CryptoFails