I've gathered all the book titles in this thread and created Amazon affiliate links (if you don't mind. Otherwise you still have all the titles together :-) )

A Pattern Language, Alexander and Ishikawa and Silverstein http://amzn.to/2s9aSSc

Advanced Programming in the Unix Environment , Stevens http://amzn.to/2qPOMjN

Algorithmics: the Spirit of Computing, Harel http://amzn.to/2rW5FNS

Applied Crytography, Wiley http://amzn.to/2rsULxS

Clean Code, Martin http://amzn.to/2sIOWtQ

Clean Coder, Martin http://amzn.to/2rWgbEP

Code Complete, McConnel http://amzn.to/2qSUIwE

Code: The Hidden Language of Computer Hardware and Software, Petzold http://amzn.to/2rWfR9d

Coders at Work, Seibel http://amzn.to/2qPCasZ

Compilers: Principles, Techniques, & Tools, Aho http://amzn.to/2rCSUVA

Computer Systems: A Programmer's Perspective, O'Hallaron and Bryant http://amzn.to/2qPY5jH

Data Flow Analysis: Theory and Practice, Khedker http://amzn.to/2qTnSvr

Dependency Injection in .NET, Seemann http://amzn.to/2rCz0tV

Domain Driven Design, Evans http://amzn.to/2sIGM4N

Fundamentals of Wireless Communication, Tse and Viswanath http://amzn.to/2rCTmTM

Genetic Programming: An Intrduction, Banzhaf http://amzn.to/2s9sdut

Head First Design Patterns, O'Reilly http://amzn.to/2rCISUB

Implementing Domain-Driven Design, Vernon http://amzn.to/2qQ2G5u

Intrduction to Algorithms, CLRS http://amzn.to/2qXmSBU

Introduction to General Systems Thinking, Weinberg http://amzn.to/2qTuGJw

Joy of Clojure, Fogus and Houser http://amzn.to/2qPL4qr

Let over Lambda, Hoyte http://amzn.to/2rWljcp

Operating Systems: Design and Implementation, Tanenbaum http://amzn.to/2rKudsw

Parsing Techniques, Grune and Jacobs http://amzn.to/2rKNXfn

Peopleware: Productive Projects and Teams, DeMarco and Lister http://amzn.to/2qTu86F

Programming Pearls, Bentley http://amzn.to/2sIRPe9

Software Process Design: Out of the Tar Pit, McGraw-Hill http://amzn.to/2rVX0v0

Software Runaways, Glass http://amzn.to/2qT2mHn

Sorting and Searching, Knuth http://amzn.to/2qQ4NWQ

Structure and Interpretation of Computer Programs, Abelson and Sussman http://amzn.to/2qTflsk

The Art of Unit Testing, Manning http://amzn.to/2rsERDu

The Art of Unix Programming, ESR http://amzn.to/2sIAXUZ

The Design of Design: Essays from a Computer Scientist, Brooks http://amzn.to/2rsPjev

The Effective Engineer, Lau http://amzn.to/2s9fY0X

The Elements of Style, Strunk and White http://amzn.to/2svB3Qz

The Healthy Programmer, Kutner http://amzn.to/2qQ2MtQ

The Linux Programming Interface, Kerrisk http://amzn.to/2rsF8Xi

The Mythical Man-Month, Brooks http://amzn.to/2rt0dAR

The Practice of Programming, Kernighan and Pike http://amzn.to/2qTje0C

The Pragmatic Programmer, Hunt and Thomas http://amzn.to/2s9dlvS

The Psychology of Computer Programming, Weinberg http://amzn.to/2rsPypy

Transaction Processing: Concepts and Techniques, Gray and Reuter http://amzn.to/

Types and Programming Languages, Pierce http://amzn.to/2qT2d6G

Understanding MySQL Internals, Pachev http://amzn.to/2svXuFo

Working Effectively with Legacy Code, Feathers http://amzn.to/2sIr09R

Zen of graphics programming, Abrash http://amzn.to/2rKIW6Q

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.

Good, but a little outdated. For general systems overview, as well as introduction to UNIX architecture, I'd actually recommend my textbook, which is the CMU intro systems book, Computer Systems: A Programmer's Perspective[1]. For OS theory, our OS/advanced OS textbooks are fine, but for actual implementation my coworkers recommended The Design of the UNIX Operating System[2], Linux System Programming[3], and Understanding the Linux Kernel[4].

[1] http://www.amazon.com/Computer-Systems-Programmers-Randal-Br...

[2] http://www.amazon.com/Design-Operating-System-Prentice-Softw...

[3] http://oreilly.com/catalog/9780596009588/

[4] http://oreilly.com/catalog/9780596005658/