[enzolovesbacon]

Although it doesn't have PGP/GnuPG, I found "The Architecture of Open Source Applications" to be very interesting and something that should be spread out more.

My work demanded me to read the ITK and VTK parts. Git and GDB are also very nice.

http://aosabook.org/en/index.html

[kqr]

Ooh, ooh, ooh they're partly by Greg Wilson! I'm a huge fan of him! Shame they don't cover GnuPG. :(