I have been keeping a list of books I used to augment my CS Masters Degree courses on various topics, here are the relevant ones I have found useful for the topics you have listed:

--Computer Organization--:

Computer Systems: A Programmer's Perspective http://www.amazon.com/Computer-Systems-Programmers-Randal-Br...

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.

--Computer Security--:

Kernel Exploitation: Attacking the Core http://www.amazon.com/Guide-Kernel-Exploitation-Attacking-Co...

Most 'hacking' books are goofy. This one is very good and doubles nicely as a hackers operating systems text.

Web Application Hackers Handbook http://www.amazon.com/Web-Application-Hackers-Handbook-Disco...

Very nice overview for web concerns.

--Operating Systems-:

Operating System Design and Implementation http://www.amazon.com/Operating-Systems-Design-Implementatio...

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 http://www.amazon.com/Linux-Kernel-Development-Robert-Love/d...

I used this to get a feel for the monolithic implementations of topics covered by Tanenbaum.

--Networking--:

TCP/IP Illustrated Series. More than you would ever want to know.

Try this book ( http://www.amazon.com/Operating-Systems-Design-Implementatio... ).

It is written be Andrew S Tanenbaum, the author of minix. The book contains whole of minix source code. Nothing beats learning from reading actual codes. Linus Torvalds was inspired by this book. In his autobiography "Just For Fun", Torvalds describes it as "the book that launched me to new heights".

OSDev ( http://wiki.osdev.org/Main_Page ) has a bunch of great stuff. Start at the top and work your way down.

Also, Operating Systems Design and Implementation, aka the Minix book, is an amazing resource.( http://www.amazon.com/Operating-Systems-Design-Implementatio... )

Actually, I'd recommend the latest version of OSDI, which is fairly recent, and contains the complete source for MINIX3 (in text form, and on CD): http://www.amazon.com/Operating-Systems-Design-Implementatio...