I'm playing through Broken Sword (Director's Cut) for the first time. I was struck by how much I enjoyed the two cryptography puzzles I've encountered so far. Can anyone recommend other games (or maybe even websites, puzzle books, etc.) that offer similar cryptography puzzles?

I liked them too, but I don't remember them being present in other games - and I really like puzzle games.

The Layton series probably has some of them (but there's so much puzzles there I forgot what 90% of them are).

Wasn't there a decryption mini-game in Sid Meier's Covert Action?

I'm not 100% sure it qualifies, as I don't remember it perfectly, but maybe Sanitarium had one of such puzzles in it.

EXperience 112 (aka, The Experiment 112) by Lexis Numérique has some cryptology in it and it's a game i trully enjoyed inspite the less than stellar ending. I've been meaning to replay it for a while now and Nordic Games currently hold the rights, so gog, chop chop ;)

If you enjoy cipher cracking there's a huge community of crackers that compete internationally all the time.

You also might enjoy this book: http://www.amazon.com/Code-Book-Science-Secrecy-Cryptography/dp/0385495323

I'm not sure how much cryptography is involved, but the DC3 Digital Forensics Challenge might tickle your fancy.