There are a lot of really good books about cryptography now.
This book is the best one that I've seen for coverage of the pitfalls of implementation.
http://www.amazon.com/Modern-Cryptography-Practice-Hewlett-P...
> I've seen you recommend GPGME previously.
I missed the context in which tptacek was recommending GPGME, but if your problem is something other than authenticating downloaded packages or signing and encrypting email, designing with GPG as a 'primitive' is probably not such a great idea. I have seen some attempts to repurpose GPG into new applications and every time these protocols have been badly flawed because the authors don't even realize that they are inventing a brand new protocol.
Last fun book : http://www.amazon.com/Woken-Furies-Takeshi-Kovacs-Novels/dp/...
I can't resist the body swapping stuff ever since reading Lord of Light as a kid