Pretty much everything from Les cent livres du siècle and Les 100 meilleurs livres de tous les temps. See also Quels sont les classiques littéraires à lire absolument ?, 100 Books to Read in a Lifetime, Alan Kay from Viewpoints Research Institute recommends his reading list for beginners, and many other similar lists. Derek Sivers' Books I've read seems to be a really good list (for non-fiction books). Five Books seems to be a good resource as well. My reference as of 2020 will be The Greatest Books, which is an aggregated list generated from more than a hundred individual lists.
Atheism / religion
- Scott Atran, "In Gods We Trust: The Evolutionary Landscape of Religion" (mentioned by Carlo Strenger in "The Fear of Insignificance: Searching for Meaning in the Twenty-First Century")
- Richard Carrier, "On the Historicity of Jesus: Why We Might Have Reason for Doubt" (this seems to be a serious book on the topic of the historicity of Jesus - no conspiracy theories, etc.)
- André Comte-Sponville, "L'esprit de l'athéisme : Introduction à une spiritualité sans Dieu" (Comte-Sponville sounds like an "old atheist", who thinks that religion can be good - e.g. lead to a more moral life)
- David Fitzgerald, "Nailed: Ten Christian Myths That Show Jesus Never Existed at All" (is this as seriously researched as Carrier's book?)
- Caroline Fourest, "Tirs croisés : La laïcité à l'épreuve des intégrismes juif, chrétien et musulman" (recommended by @ArianeBeldi)
- Philip Kitcher, "Life After Faith: The Case for Secular Humanism"
- George Levine, "The Joy of Secularism: 11 Essays for How We Live Now"
- David Mills, "Atheist Universe"
- David Niose, "Nonbeliever Nation: The Rise of Secular Americans" (reviewed on Friendly Atheist)
- Victor J. Stenger, "God: The Failed Hypothesis" (Victor J. Stenger is one of the "New Atheists", he died in 2014)
- Bible (e-book, really long to read?)
- authors listed in "50 Top Atheists in the World Today" (2011) (Peter Singer, etc.)
Biography
- Christopher Hitchens, "Hitch-22: A Memoir"
Business / entrepreneurship
- Jason Fried, "Rework" (mentioned by @epsitec)
- Michael A. Hiltzik, "Dealers of Lightning: Xerox PARC and the Dawn of the Computer Age" (recommended by @akosma)
- Christopher Locke, Rick Levine, Doc Searls & David Weinberger, "The Cluetrain Manifesto: The End of Business as Usual"
- Rowan Manahan, "Where's My Oasis?: The Essential Handbook for Everyone Wanting that Perfect Job"
- Don Norman, "The Design of Everyday Things: Revised and Expanded Edition" (recommended by @akosma)
- OCTO Technology, "Partageons Ce Qui Nous Departage"
- Paul Sloane, "The Innovative Leader: How to Inspire Your Team and Drive Creativity"
Comics
- Andy Fischli (only available in German?)
- F'murr (already read a lot of his works; e.g. "Bêêêêstes of le Génie des alpages" contains previously unreleased material)
- Winsor McCay, "Little Nemo"
- Guillermo Mordillo
- François Schuiten & Benoît Peeters, "L'archiviste"
- François Schuiten & Benoît Peeters, "L'écho des cités"
- François Schuiten & Benoît Peeters, "Le guide des cités"
- François Schuiten & Benoît Peeters, "L'ombre d'un homme"
- François Schuiten & Benoît Peeters, "La route d'Armilia"
- François Schuiten & Benoît Peeters, "Voyages en utopie"
- François Schuiten & Benoît Peeters, other "Les Cités obscures" stories that I haven't read yet
- Lewis Trondheim (I need to read all his works)
Computer science / software
- Jon Bentley, "Programming Pearls"
- Frederick P. Brooks Jr., "The Mythical Man-Month, Anniversary Edition: Essays On Software Engineering" (recommended by @akosma)
- Raymond Chen, "The Old New Thing: Practical Development Throughout the Evolution of Windows" (recommended by @akosma)
- Thomas Cormen, "Introduction to Algorithms"
- Tom DeMarco, "Peopleware: Productive Projects and Teams" (recommended by @akosma)
- Eric Evans, "Domain-Driven Design: Tackling Complexity in the Heart of Software" (recommended by @behaghel)
- Erich Gamma, etc., "Design Patterns: Elements of Reusable Object-Oriented Software"
- Imran Ghory, "Reinforcement learning in board games"
- Robert L. Glass, "Facts and Fallacies of Software Engineering" (recommended by @akosma)
- Andy Hertzfeld, "Revolution in The Valley: The Insanely Great Story of How the Mac Was Made" (recommended by @akosma)
- Steve Krug, "Don't Make Me Think: A Common Sense Approach to Web Usability" (recommended by @behaghel?)
- F. William Lawvere & Stephen H. Schanuel, "Conceptual Mathematics: A First Introduction to Categories"
- Robert C. Martin, "Clean Code: A Handbook of Agile Software Craftsmanship"
- Steve McConnell, "Code Complete: A Practical Handbook of Software Construction"
- Benjamin C. Pierce, "Types and Programming Languages" (recommended by @icassina, quite "academic"/complex; see also code in Scala)
- Eric S. Raymond, "The Cathedral & the Bazaar: Musings on Linux and Open Source by an Accidental Revolutionary" (recommended by @akosma)
- David Rice, "Geekonomics: The Real Cost of Insecure Software" (recommended by @akosma)
- Fabien Sanglard, "Game Engine Black Book: Doom" (free ebook)
- Harold Simmons, "An Introduction to Category Theory" (also recommended by @icassina?)
- Joel Spolsky, "The Best Software Writing I" (belonging to @ebruchez)
- Steve Weber, "The Success of Open Source" (recommended by @akosma)
- Gerald Weinberg, "The Psychology of Computer Programming: Silver Anniversary" (recommended by @akosma)
- see also "What is the single most influential book every programmer should read?"
- see also "What non-programming books should programmers read?"
Economics
- Jacques Attali, "La crise, et après ?" and other essays (economics, finance, etc.) (was this recommended by @behaghel?)
- Ronald Findlay, "Power and Plenty: Trade, War, and the World Economy in the Second Millennium (Princeton Economic History of the Western World)" (recommended by Christoph G.)
- Milton Friedman & Rose Friedman, "Free to Choose" (recommended by @avernet)
- Thomas Piketty, "Le Capital au XXIe siècle" (long book - 970 pages -, recommended by @danielmiessler)
- Nassim Nicholas Taleb, "Antifragile: Things that Gain from Disorder"
- Charles Wheelan, "Naked Economics: Undressing the Dismal Science" (recommended by @danielmiessler)
Education
- Martha C. Nussbaum, "Cultivating Humanity: A Classical Defense of Reform in Liberal Education" (mentioned by Carlo Strenger in "The Fear of Insignificance")
Essays
- Christopher Hitchens, "Arguably: Essays by Christopher Hitchens"
- Tim Kreider, "We Learn Nothing: Essays" (recommended by @tferriss)
- Daniel Pennac, "Comme un roman" (already read, to read again)
Fiction
- Scott Adams, "The Religion War"
- Isaac Asimov, "Foundation" (series) (science fiction classic)
- Gabriel Bá & Fábio Moon, "Daytripper" (recommended by @avernet)
- René Barjavel, "La Nuit des temps" (recommended by @behaghel)
- René Barjavel, "Le Grand Secret" (recommended by @behaghel)
- René Barjavel, "Ravage" (recommended by @behaghel)
- Emily Brontë, "Wuthering Heights"
- S. Corinna Bille, "La Fraise Noire" (read a long time ago?)
- Douglas Coupland, "Microserfs"
- Roald Dahl, short stories not included in "The Collected Short Stories of Roald Dahl"
- Antoine de Saint-Exupéry "Vol de Nuit", etc.
- Friedrich Dürrenmatt, "Der Tunnel" (short story, mentioned by @icassina)
- Antoine Galland, "Les Milles et Une Nuits"
- Romain Gary, "La Vie devant soi" (recommended by a colleague)
- William Gibson, "Neuromancer" (science fiction classic, recommended by @JeromeCaillet)
- Frank Herbert, "Dune" (series) (science fiction classic)
- Franz Kafka, "L'amérique" (read during the 90s)
- Frank Kafka, "Le château" (read in 2001)
- Franz Kafka, "Le procès" (read in 2004)
- Cormac McCarthy, "The Road" (saw the movie in 2010 and liked it)
- Ursula K. Le Guin, "The Found and the Lost: The Collected Novellas of Ursula K. Le Guin" (I'm not sure where to start, are there better collections?)
- Ursula K. Le Guin, "The Dispossessed" (can it be read independently?)
- Bill Moody, "Sur les traces de Chet Baker"
- Amélie Nothomb, "Acide sulfurique" (recommended by Miriam)
- H. P. Lovecraft, "The Complete Works of H.P. Lovecraft"
- Terry Pratchett, "The Colour of Magic" (recommended by François in 2015)
- Terry Pratchett, "The Dark Side of the Sun" (recommended by François?)
- Terry Pratchett, "Strata" (recommended by François?)
- Jean-Paul Sartre, "Le mur" (read during the 90s?)
- Dan Simmons, "Hyperion" (science fiction classic, recommended by @JeromeCaillet)
- Neil Stephenson, "Cryptonomicon" (recommended by @ebruchez)
- Charles Stross, "Singularity Sky"
- Boris Vian, "L'Arrache-cœur"
- Boris Vian, "L'Équarrissage pour tous"
- Boris Vian, "Et on tuera tous les affreux"
- Boris Vian, "Le Goûter des généraux"
- Boris Vian, "L'Herbe rouge"
- Boris Vian, "J'irai cracher sur vos tombes"
- Boris Vian, "Chansons", "Nouvelles", "Poèmes", "Textes sur le jazz" (sections from a Boris Vian collection I received as a gift)
- Bernard Werber, "Les fourmis"
- Bernard Werber, "Nous les Dieux"
Health
- R. Barker Bausell, "Snake Oil Science: The Truth about Complementary and Alternative Medicine"
- Jean Brissonnet, "Les pseudo-médecines : Un serment d'hypocrites"
- Edzard Ernst, "Healing, Hype, or Harm?: A Critical Analysis of Complementary or Alternative Medicine"
- Mikhail Tombak, "Can We Live 150 Years?"
History / anthropology
- Jared Diamond, "Collapse: How Societies Choose to Fail or Succeed" (recommended by Franck?)
- Jared Diamond, "Guns, Germs, and Steel: The Fates of Human Societies" (recommended by Franck?)
Humor
- Pierre Desproges, "Dictionnaire superflu à l'usage de l'élite et des biens nantis" (and others)
Interviews
- Maurice Chappaz, "À-Dieu-Vat !"
Meditation
- Bhante Gunaratana, "Mindfulness In Plain English"
- Alan Watts, "Out of Your Mind: Essential Listening from the Alan Watts Audio Archives" (audio book, recommended by @avernet)
Misc
- Florence Braunstein & Jean-François Pépin, "La Culture générale pour les Nuls"
- Ben Schott, "Schott's Quintessential Miscellany"
- William Strunk & E.B. White, "The Elements of Style"
- Eric Voutaz, "Pincées d'espoir" (received from Eric)
Music
- Frank Alkyer, "The Miles Davis Reader"
- Jan Swafford, "Language of the Spirit: An Introduction to Classical Music" (looks like a good introduction to classical music)
Parenthood
- Jennifer Senior, "All Joy and No Fun: The Paradox of Modern Parenthood"
Personal development
- David Allen, "Getting Things Done" (already read - read again? - or read the 2015 version)
- David Allen, "Making It All Work"
- Leo Babauta, "The One Skill: How Mastering the Art of Letting Go Will Change Your Life" (free book, mentioned by @avernet)
- Leo Babauta, "Zen To Done"
- Travis Bradberry & Jean Greaves, "Emotional Intelligence 2.0"
- Dale Carnegie, "How To Win Friends and Influence People" (listed on Hacker News)
- Ray Dalio, "Principles: Life and Work" (recommended on @Coursera)
- Arvind Devalia, "Get the Life You Love and Live It"
- Tim Ferriss, "Tools of Titans: The Tactics, Routines, and Habits of Billionaires, Icons, and World-Class Performers" (really interesting or not?)
- Tim Ferriss, "Tribe of Mentors: Short Life Advice from the Best in the World" (really interesting or not?)
- Jonathan Fields, "Career Renegade: How to Make a Great Living Doing What You Love"
- P.M. Forni, "The Thinking Life: How to Thrive in the Age of Distraction"
- Dan Harris, "10% Happier: How I Tamed the Voice in My Head, Reduced Stress Without Losing My Edge, and Found Self-Help That Actually Works" (recommended by @PeterAttiamd)
- Gordon MacKenzie, "Orbiting the Giant Hairball: A Corporate Fool's Guide to Surviving with Grace"
- Eric Maisel, "The Creativity Book: A Year's Worth of Inspiration and Guidance"
- Mark Manson, "Models: Attract Women Through Honesty" (recommended by @danielmiessler)
- David McRaney, "You Are Now Less Dumb: How to Conquer Mob Mentality, How to Buy Happiness, and All the Other Ways to Outsmart Yourself"
- Becki Saltzman, "Living Curiously: How to Use Curiosity to be Remarkable and Do Good Stuff" (recommended by @gschaer)
- Eckhart Tolle, "A New Earth"
Philosophy
- Simon Blackburn, "Think: A Compelling Introduction to Philosophy" (Blackburn is an atheist; he doesn't agree with Harris on morality)
- Russell Blackford & Damien Broderick, "Intelligence Unbound: The Future of Uploaded and Machine Minds" (mentioned on kurzweilai.net)
- Jean Bricmont & Alan Sokal, "Intellectual Impostures" (recommended by Stephen Law - books about pseudoscience; see also the original French version, "Impostures intellectuelles")
- David Chalmers, "The Conscious Mind: In Search of a Fundamental Theory" (and others) (seems to have a very weird view on consciousness - and philosophical zombies - not necessarily interesting)
- Brian Christian, "The Most Human Human: What Talking with Computers Teaches Us About What It Means to Be Alive"
- Paul Davies, "The Mind Of God"
- Daniel Dennett, "Freedom Evolves" (and others) (but I really don't agree with him on free will!)
- Will Durant, "The Story of Philosophy: The Lives and Opinions of the World's Greatest Philosophers"
- Michael S. A. Graziano, "Consciousness and the Social Brain" (summarized by @SelfAwarePatter on his blog)
- Douglas Richard Hofstadter, "I Am a Strange Loop"
- Bruce Hood, "The Self Illusion: How the Social Brain Creates Identity" (interviewed by @SamHarrisOrg)
- Julian Jaynes, "The Origin of Consciousness in the Breakdown of the Bicameral Mind"
- William MacAskill, "Doing Good Better: Effective Altruism and a Radical New Way to Make a Difference" (interviewed by @SamHarrisOrg)
- Bryan Magee, "The Great Philosophers: An Introduction to Western Philosophy" (was Magee atheist?)
- Jacques Monod, "Le Hasard et la Nécessité. Essai sur la philosophie naturelle de la biologie moderne" (Monod was Camus' friend; this book seems to be a good complement to "The Selfish Gene")
- Thomas Nagel, "The Last Word" (recommended by @SamHarrisOrg)
- Robert Nozick, "Philosophical Explanations"
- Richard Oerton, "The Nonsense of Free Will: Facing Up to a False Belief" (recommended by @SamHarrisOrg)
- Michel Onfray, "Contre-histoire de la philosophie" (several volumes)
- Donald Palmer, "Looking at Philosophy: The Unbearable Heaviness of Philosophy Made Lighter" (easy to read, comics, etc.)
- Derek Parfit, "Reasons and Persons" (recommended by @SamHarrisOrg and @willmacaskill)
- Roger Penrose, "The Emperor's New Mind"
- Roger Penrose, "Shadows of the Mind: A Search for the Missing Science of Consciousness" (and others)
- Massimo Pigliucci, "Answers for Aristotle: How Science and Philosophy Can Lead Us to A More Meaningful Life" (Massimo Pigliucci is a philosopher fighting scientism among "New Atheists" such as Sam Harris, etc.)
- Robert M. Pirsig, "Zen and the Art of Motorcycle Maintenance: An Inquiry into Values"
- Jacques Pitrat, "Artificial Ethics: Moral Conscience, Awareness and Consciencousness"
- W. V. Quine & J. S. Ullian, "The Web of Belief"
- Jean-François Revel & Matthieu Ricard, "Le moine et le philosophe" (mentioned by Carlo Strenger in "The Fear of Insignificance")
- Michael Sandel, "Justice: What's the Right Thing to Do?" (recommended by Massimo Pigliucci in his negative review of "The Moral Landscape")
- Peter Singer, "The Most Good You Can Do: How Effective Altruism Is Changing Ideas About Living Ethically"
- Nassim Nicholas Taleb, "The Black Swan: The Impact of the Highly Improbable"
- Theodore Schick & Lewis Vaughn, "How to Think About Weird Things: Critical Thinking for a New Age" (recommended by Peter Boghossian, author of "A Manual for Creating Atheists")
Physics / cosmology
- Bill Bryson, "A Short History Of Nearly Everything"
- Richard P. Feynman, "QED: The Strange Theory of Light and Matter" (recommended on Quora)
- Richard P. Feynman, "What Do You Care What Other People Think?"
- Brian Greene, "The Elegant Universe: Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory"
- Brian Greene, "The Fabric of the Cosmos: Space, Time, and the Texture of Reality"
- Stephen Hawking, "The Universe in a Nutshell"
- Michio Kaku, "Parallel Worlds: A Journey Through Creation, Higher Dimensions, and the Future of the Cosmos"
- Manjit Kumar, "Quantum: Einstein, Bohr and the Great Debate About the Nature of Reality" (recommended by dad)
- David Lindley, "Where Does The Weirdness Go?: Why Quantum Mechanics Is Strange, But Not As Strange As You Think" (recommended on Quora)
- Bruce Rosenblum & Fred Kuttner, "Quantum Enigma: Physics Encounters Consciousness"
- Charles Seife, "Decoding the Universe: How the New Science of Information Is Explaining Everything in the Cosmos, from Our Brains to Black Holes"
- Max Tegmark, "Our Mathematical Universe: My Quest for the Ultimate Nature of Reality" (summarized by @SelfAwarePatter on his blog)
- that old book my grandparents gave me when I was 8-10 years old
Psychology
- Eric B. Baum, "What Is Thought?" (recommended by @r3mix)
- Ed Diener, "Happiness: Unlocking the Mysteries of Psychological Wealth" (recommended on @Coursera)
- Robert H. Frank, "Passions Within Reason: The Strategic Role of the Emotions" (recommended by @verybadwizards, not available as e-book as of Jan. 2017)
- Winifred Gallagher, "Rapt: Attention and the Focused Life"
- Daniel Goleman, "Emotional Intelligence: 10th Anniversary Edition; Why It Can Matter More Than IQ"
- Jonathan Haidt, "The Happiness Hypothesis: Putting Ancient Wisdom to the Test of Modern Science" (had a really good discussion with @SamHarrisOrg on his podcast)
- Michael John Harris, "The End of Absence: Reclaiming What We've Lost in a World of Constant Connection"
- Robert-Vincent Joule & Jean-Léon Beauvois, "La soumission librement consentie" (read "Petit traité de manipulation à l'usage des honnêtes gens" from them)
- Daniel Kahneman, "Thinking, Fast and Slow" (recommended by @mistertricker)
- Robert Levine, "The Power of Persuasion: How We're Bought and Sold" (recommended by @willmacaskill)
- Barry Schwartz, "The Paradox of Choice: Why More Is Less"
- Carol Tavris & Elliot Aronson, "Mistakes Were Made (But Not by Me): Why We Justify Foolish Beliefs, Bad Decisions, and Hurtful Acts" (recommended by @PeterAttiamd)
Science
- Richard Dawkins, "The Extended Phenotype" (considered by Richard Dawkins himself as his best book)
- Richard Dawkins, "The Magic of Reality: How We Know What's Really True"
- Jordan Ellenberg, "How Not to Be Wrong: The Power of Mathematical Thinking"
- Ben Goldacre, "I Think You'll Find It's a Bit More Complicated Than That"
- Douglas Richard Hofstadter, "Gödel, Escher, Bach: An Eternal Golden Braid" (recommended by @aloiscochard)
- Darrell Huff, "How to Lie with Statistics" (recommended by @behaghel)
- Matt Ridley, "The Evolution of Everything: How New Ideas Emerge"
- Matt Ridley, "The Red Queen: Sex and the Evolution of Human Nature" (recommended by @danielmiessler)
Social sciences / sociology / politics
- Noam Chomsky, "Understanding Power: The Indispensible Chomsky" (one of this best books, apparently)
- Caroline Fourest, "Le choc des préjugés : L'impasse des postures sécuritaires et victimaires" (recommended by @ArianeBeldi)
- Normand Baillargeon, "Petit cours d'autodéfense intellectuelle"
- Thomas Friedman, "The World Is Flat: A Brief History of the Twenty-First Century"
- Eric Hoffer, "The True Believer: Thoughts on the Nature of Mass Movements"
- A. des Isnards & T. Zuber, "L'Open Space m'a tuer"
- Johan Norberg, "Progress: Ten Reasons to Look Forward to the Future"
Switzerland
- Maurice Chappaz, "Portrait des Valaisans"
- ?, "Forces Motrices de Mauvoisin S.A. : Nos 50 Ans"
Technology
- James Barrat, "Our Final Invention: Artificial Intelligence and the End of the Human Era" (recommended by @SamHarrisOrg)
- Nick Bostrom, "Superintelligence: Paths, Dangers, Strategies" (recommended by @SamHarrisOrg)
- Erik Brynjolfsson & Andrew McAfee, "Race Against The Machine: How the Digital Revolution is Accelerating Innovation, Driving Productivity, and Irreversibly Transforming Employment and the Economy"
- Peter H. Diamandis & Steven Kotler, "Abundance: The Future Is Better Than You Think" (recommended by Ray Kurzweil)
- Douglas Rushkoff, "Throwing Rocks at the Google Bus: How Growth Became the Enemy of Prosperity"
Travel
- Patricia Schultz, "1,000 Places to See Before You Die: A Traveler's Life List"