Lectures:
Note that there is also Maple code for elliptic curves available under the name Apecs.
Contents:
New: All lecture notes combined into one pdf
Lecture 1 (Th 7.10.): Overview (draft text)
Lecture 2 (Fr 8.10.): Properties of the integers; primes and divisibility.
Problems Class/Lecture (Tu 12.10.) and Lecture 3 (Th 14.10.): Greatest common divisor, division algorithm, Euclidean algorithm.
Lecture 4 (Tu 19.10.) Fundamental Theorem of Arithmetic. Are there infinitely many primes?
Lecture 5 (Th 21.10.) (Towards the) Prime Number Theorem.
Lecture 6 (Tu 26.10.) The Prime Number Theorem and primes in arithmetic progression.
Lecture 7 (Th 28.10.) Congruences, towards Fermat's Little Theorem.
Lecture 8 (Tu 2.11.) Fermat's Little Theorem, linear congruences, Euler-Fermat, Euler phi function.
Lecture 9 (Th 4.11.) Wilson's Theorem, Chinese Remainder Theorem.
Lecture 10 (Tu 9.11.) Chinese Remainder Theorem, Applications.
Lecture 11 (Th 11.11.) Modular exponentiation, towards public key cryptography.
Lecture 12 (Tu 16.11.) Diffie-Hellman key exchange, computing k-th roots modulo m, trapdoor function.
Lecture 13 (Th 18.11.) Computing k-th roots modulo m (algorithm), RSA.
Lecture 14 (Tu 23.11.) Attacking/cracking RSA. Factorization methods.
Lecture 15 (Th 25.11.) Factoring with high probability. Towards primitive roots modulo a prime.
Lecture 16 (Tu 30.11.) Primitive roots modulo a prime. The discrete logarithm problem.
Lecture 17 (Th 2.12.) The discrete logarithm problem. Index calculus.
Lecture 18 (Tu 7.12.) Quadratic Residues.
Lecture 19 (Th 9.12.) Legendre symbol, Euler criterion, (towards the) quadratic reciprocity law.
Lecture 20 (Tu 14.12.) Statement and proof of the quadratic reciprocity law. Applications.
Assignments:  Set and collected every other Tuesday.
[Hints: for Sheet 3, Q5c) list (and then sum) all the divisors of 2^k*p, for p a prime, by grouping them into those which are divisible by p and those which are not; for Sheet 4, Q6) first show the congruence that you obtain from squaring both sides; then recall Wilson's Theorem and pair numbers off appropriately.]  
A typo in Q 5a): it should read $n>1$, obviously. A second typo is a missing assumption in Q6) where p is supposed to be a prime. (Both spotted by Chris Moore.)
Yet another one in Q1c) from Sheet 4: "integers mod 100" should read "integer squares mod 100".
Hint for Q7 from Sheet 4: think Fermat's Little Theorem.
A typo in Q 5a) of Sheet 6: the encryption exponent should be 19 rather than 9.
Moreover, the modulus in the public key in 5b) is far too small. Please use the key (n,e)= (100160063,17) from the lectures instead or, better still, produce one that allows you to encode your name in full. (Both spotted by Aaron Paxton.)
For the homework please also answer the following question for Q5a): why would an encryption exponent 9 be a bad idea for the given modulus?
Typo in Q1a): 3^(m/32) should read 3^(m/16) [spotted by Aaron Paxton, yet again]
Problems:
(Almost) every week a new sheet will be added, and eventually solutions will be given to most of the problems.
Reading suggestions:
One of the most eminent number theorists in the last century was Andre Weil who has written one very nice introductory text
Furthermore, here you can find a large library of links (some are already outdated, alas) to online notes (some of them in French, German, Dutch or even Greek!), the more elementary of which cover quite similar number theoretic ground as the lectures. Not each source deals with cryptographic topics, though.