Bletchley – A Collection of Practical Cryptanalysis Tools
code.google.com
code.google.com
I don't know how this fares when it comes to blackbox crypto pen-testing, but I must admit I shudder at the thought of blackbox crypto pen-testing.
[1] http://blog.ram.rachum.com/post/56061414423/the-interactive-...
For the record, Cryptography Engineering is his latest book on the topic, and it is a good one. But like all technical books, it's also a little out of date.
0: http://www.amazon.com/Cryptography-Engineering-Principles-Pr...
Coursera also has three cryptography classes: Cryptography I, Cryptography II, and Intro to Cryptography (all taught by Dan Boneh).
And, of course, Bruce Schneier's Cryptography Engineering (Applied Engineering is somewhat deprecated).