A lot of the books have overlapping themes, so I just tried to group them according to their central ideology. I'm just going off my own books, so feel free to suggest additions.

Libertarianism:
- 1984 and Animal Farm by George Orwell
- The Moon is a Harsh Mistress by Robert A. Heinlein
- Liberty Defined by Ron Paul
- Brave New World by Aldous Huxley
- Atlas Shrugged by Ayn Rand
- Free to Choose by Milton Friedman
- The Age of Turbulence: Adventures in a New World by Alan Greenspan

Capitalism:
- Capitalism and Freedom by Milton Friedman
- The Wealth of Nations by Adam Smith
- Austrian Economics: A Primer by Dr. Eamonn Butler
- The General Theory of Employment, Interest and Money by John Maynard Keynes
- The Failure of New Economics: An Analysis of the Keynesian Fallacies by Henry Hazlitt
- End the Fed by Ron Paul
- The Federal Reserve and the Financial Crisis by Ben S. Bernanke
- Boom and Bust Banking: the Causes and Cures of the Great Recession by David Beckworth

Authoritarianism:
- Mein Kampf by Adolf Hitler

Conservatism:
- The Quest for Cosmic Justice by Thomas Sowell
- Liberal Fascism by Jonah Goldberg
- American Conservatism: An Encyclopedia by Bruce Fohnen

Liberalism:
- FDR by Jean Edward Smith

Socialism:
- Profit Over People: Neoliberalism and the Global Order by Noam Chomsky
- Occupy by Noam Chomsky
- The Conquest of Bread by Pyotr Kropotkin
- The Communist Manifesto by Karl Marx

Philosophy:
- Thus Spake Zarathustra by Friedrich Nietzsche
- Beyond Good and Evil by Friedrich Nietzsche
- Anarchism by Ruth Kinna
- Enquiries Concerning Human Understanding and Concerning the Principles of Morals by David Hume
- The World as Will and Representation by Arthur Schopenhauer
- Republic by Plato
- The Moral Landscape by Sam Harris
- Zen and the Art of Motorcycle Maintenance by Robert M. Pirsig
- The Prince by Niccolo Machiavelli
- Leviathan by Thomas Hobbes
- Common Sense by Thomas Paine

Religion:
- God is Not Great by Christopher Hitchens
- The God Delusion by Richard Dawkins

Common Sense?

By Thomas Paine?

Yes

Under philosophy?

The Spirit of the Laws, The Persian Letters, The Second Treatise on Civil Government

I'll list them as they come to me. I'm a little lacking on the philosophical stuff. I'm decently read on physics stuff and am well aware that most of this won't interest anyone other than me.

GΓΆdel, Escher, Bach - Douglas Hofstadter (any one interested in AI  or just really interesting shit in general definitely should read this)
The Fabric of Reality - David Deutsch (popular level, a lot of this stuff is really far out but interesting none the less)
Six Easy Pieces - Richard Feynman(good introduction to some of his lectures on physics)
The Mars Trilogy - Kim Stanley Robinson ( a trilogy of books about Terraforming Mars)
The Road to Reality - Roger Penrose (not for the faint of heart, thousand page book, the first 300 and something pages of which is dedicated entirely to the math needed to understand the other 700)
I Am A Strange Loop - Douglas Hofstadter (expounds on the concept of strange loops developed in EGB)
The Trouble With Physics - Lee Smolin (explains many of the problems with the string approach to quantum gravity in a way that's easy to digest for laymen)
Solaris - Stanislaw Lem
The Millennial Project - Marshal T. Savage (lays out in detail how humanity can go about large scale colonization of space)
Not Even Wrong - Peter Woit ( first half gives possibly the most accurate account of QFT I've ever seen in a popular level book, second half gives several arguments as to why string theory is a failed research program and is "Not even wrong")

I'm sure I'm biased, but The God Delusion is widely recognized as highly flawed, biased, and sloppy in its arguments. I never finished it because 50 pages in every argument Dawkins made could have been refuted by a 15 year old Sunday School student.

Augustine's City of God is a good foil to the two you've got listed.

I would have said this is good enough to merit a sticky even without the demand >_>

Also +100 to anyone who can actually finish Mein Kampf. It reads like a brick wall ._.

Always wanted to read Mein Kamph

You should add Ishmael by Daniel Quinn to the philosophy section. That's an insanely enlightening book.

You could make a personal development section and add these.

Goals by Brian Tracy
 -Explains how to set goals based on studies of successful people and companies goal setting principles.

Willpower by Roy F. Baumeister
 -Talks how willpower is essentially like a mental muscle and you can strengthen it by exercising discipline, and how it's influenced by glycogen levels.

A small edit, but the Communist Manifesto should be labelled as both Karl Marx and Friedrich Engels