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