I've found "Inside the Machine" by Jon Stokes to be quite a good read, though it's a bit dated by now (published 2006)

http://www.amazon.com/dp/1593271042/

For programmers I would recommend a real computer architecture textbook (e.g. http://books.google.com/books?id=57UIPoLt3tkC) instead of Stokes's analogy-laden book.

Professional Linux Kernel Architecture has a good introduction into the Linux/os nomenclature.