Computer Systems: A Programmer's Perspective
I liked this much better than Computer Organization and Design by Patterson and Hennessy which everyone has encountered at some point. The developer-centric view was very cool.
Kernel Exploitation: Attacking the Core
Most 'hacking' books are goofy. This one is very good and doubles nicely as a hackers operating systems text.
Web Application Hackers Handbook
Very nice overview for web concerns.
Operating System Design and Implementation
I don't agree with Tanenbaum's views on micro vs. monolithic kernels but this book is a great mix of theory and implementation.
Linux Kernel Devleopment
I used this to get a feel for the monolithic implementations of topics covered by Tanenbaum.
TCP/IP Illustrated Series. More than you would ever want to know.