I collected 10 lists of the Best Non-Fiction Books of All Time and combined them into one meta-list.  Here are the results: all the non-fiction books on at least two of the original source lists, organized by rank (that is, with the books on the most lists at the top).  Please note that these are not my personal opinions and I have not read all these books.

To see the same list organized chronologically, go here.

On 8 lists
Silent Spring (1962, US) – Rachel Carson
In Cold Blood (1966, US) – Truman Capote

On 6 lists
The Prince (1532, Italy) – Niccolò Machiavelli
On the Origin of Species (1859, UK) – Charles Darwin
The Elements of Style (1918, US) – William Strunk & E. B. White
A Room of One’s Own (1929, UK) – Virginia Woolf
Homage To Catalonia (1938, UK) – George Orwell
The Diary of a Young Girl (1947, The Netherlands) – Anne Frank
Bury My Heart At Wounded Knee (1970, US) – Dee Brown

On 5 lists
Speak, Memory (1951, USSR/US) – Vladimir Nabokov
The Autobiography of Malcolm X (1965, US) – Malcolm X with Alex Haley
A Brief History of Time: From the Big Bang to Black Holes (1988, UK) – Stephen Hawking

On 4 lists
The Communist Manifesto (1848, UK) – Karl Marx & Friedrich Engels
Walden (1854, US) – Henry David Thoreau
The Interpretation of Dreams (1899, Austria) – Sigmund Freud
Goodbye To All That (1929, UK) – Robert Graves
Hiroshima (1946, US) – John Hersey
The Structure of Scientific Revolutions (1962, US) – Thomas S. Kuhn
The Double Helix: A Personal Account of the Discovery of the Structure of DNA (1968, US) – James D. Watson
Slouching Towards Bethlehem (1968, US) – Joan Didion
The Electric Kool-Aid Acid Test (1968, US) – Tom Wolfe
All The President’s Men (1974, US) – Carl Bernstein & Bob Woodward
Dispatches (1977, US) – Michael Herr
The Gnostic Gospels (1979, US) – Elaine Pagels
The Right Stuff (1979, US) – Tom Wolfe
Into The Wild (1996, US) – Jon Krakauer
Guns, Germs, and Steel: The Fate of Human Societies (1997, US) – Jared Diamond
On Writing: A Memoir of The Craft (2000, US) – Stephen King
Fast Food Nation: The Dark Side of The All-American Meal (2001, US) – Eric Schlosser
Nickel and Dimed: On (Not) Getting By In America (2001, US) – Barbara Ehrenreich
The Devil in the White City: Murder, Magic, and Madness at the Fair That Changed America (2003, US) – Erik Larson
The Emperor of All Maladies: A Biography of Cancer (2010, US) – Siddhartha Mukherjee

On 3 lists
The Histories (440 BCE, Ancient Greece) – Herodotus
The Republic (c. 380 BCE, Ancient Greece) – Plato
Essays (1580, France) – Michel De Montaigne
Leviathan (1651, UK) – Thomas Hobbes
The Life of Samuel Johnson, LL.D. (1791, UK) – James Boswell
Rights of Man (1791 (Pt. 1); 1792 (Pt. 2), UK) – Thomas Paine
Democracy in America (1835 (Pt. 1), 1840 (Pt. 2), France) – Alexis de Tocqueville
On Liberty (1859, UK) – John Stuart Mill
The Varieties of Religious Experience (1902, US) – William James
Eminent Victorians (1918, US) – Lytton Strachey
Seven Pillars of Wisdom: A Triumph (1922, pub. 1926, UK) – T. E. Lawrence
The Autobiography of Alice B. Toklas (1933, US/France) – Gertrude Stein
The General Theory of Employment, Interest, and Money (1936, UK) – John Maynard Keynes
Out of Africa (1937, UK/Denmark) – Isak Dinesen
Let Us Now Praise Famous Men (1941, US) – James Agee (text) & Walker Evans (photos)
Black Boy (1945, US) – Richard Wright
The Second Sex (France, 1949) – Simone de Beauvoir
Mythologies (1957, France) – Roland Barthes
The Rise and Fall of The Third Reich: A History of Nazi Germany (1960, US) – William L. Shirer
The Guns of August (1962, US) – Barbara Tuchman
The Feminine Mystique (1963, US) – Betty Friedan
I Know Why The Caged Bird Sings (1969, US) – Maya Angelou
The Civil War: A Narrative (1974, US) – Shelby Foote
Zen and The Art of Motorcycle Maintenance: An Inquiry Into Values (1974, US) – Robert M. Pirsig
The Great War and Modern Memory (1975, US) – Paul Fussell
The Selfish Gene (1976, UK) – Richard Dawkins
Orientalism (1978, Palestine/US) – Edward W. Said
Gödel, Escher, Bach: An Eternal Golden Braid (1979, US) – Douglas Hofstadter
A People’s History of The United States (1980, US) – Howard Zinn
Maus: A Survivor’s Tale: My Father Bleed’s History (1986, US) – Art Spiegelman
And The Band Played On: Politics, People, and The Aids Epidemic (1987, US) – Randy Shilts
The Journalist and The Murderer (1990, US) – Janet Malcolm
The Beauty Myth: How Images of Beauty Are Used Against Women (1990, US) – Naomi Wolf
Midnight in the Garden of Good and Evil (1994, US) – John Berendt
The Perfect Storm: A True Story of Men Against the Sea (1997, US) – Sebastian Junger
A Supposedly Fun Thing I’ll Never Do Again: Essays and Arguments (1997, US) – David Foster Wallace
A Walk In The Woods: Rediscovering America on the Appalachian Trail (1998, US) – Bill Bryson
We Wish To Inform You That Tomorrow We Will Be Killed With Our Families: Stories from Rwanda (1998, US) – Philip Gourevitch
Moneyball: The Art of Winning an Unfair Game (2003, US) – Michael Lewis
The Omnivore’s Dilemma: A Natural History of Four Meals (2006, US) – Michael Pollan
Outliers: The Story of Success (2008, US) – Malcolm Gladwell
The Lost City of Z: A Tale of Deadly Obsession in the Amazon (2009, US) – David Grann

On 2 lists
The History of the Peloponnesian War (c. 431-410 BCE, Ancient Greece) – Thucydides
The Art of War (c. 499-400 BCE, China) – Sun Tzu (Sunzi) (attrib.)
Symposium (c. 385-370 BCE, Ancient Greece) – Plato
Analects (c. 475-221 BCE, China) – Confucius (attrib.)
Meditations (180 CE, Ancient Rome) – Marcus Aurelius
Confessions (c. 397-400 CE, Ancient Rome/Numidia) – Augustine of Hippo
The Lives of the Most Excellent Painters, Sculptors, and Architects (1550, Italy) – Giorgio Vasari
Philosophae Naturalis Principia Mathematica (1687, UK) – Isaac Newton
The Confessions (1769, pub. 1782, France/Switzerland) – Jean-Jacques Rousseau
The Wealth of Nations (1776, GB) – Adam Smith
Critique of Pure Reason (1781, Germany) – Immanuel Kant
The History of the Decline and Fall of the Roman Empire (1776-1789, GB) – Edward Gibbon
A Vindication of the Rights of Woman (1792, UK) – Mary Wollstonecraft
Narrative of the Life of Frederick Douglass, an American Slave (1845, US) – Frederick Douglass
Das Kapital: Critique of Political Economy (1867-1883, Germany/UK) – Karl Marx
The Golden Bough: A Study in Comparative Religion (1890, UK) – James George Frazer
Thus Spoke Zarathustra (1883-1891, Germany) – Friedrich Nietzsche
Up From Slavery (1901, US) – Booker T. Washington
The Souls of Black Folk (1903, US) – W.E.B. Du Bois
Relativity: The Special and General Theory (1916, Germany) – Albert Einstein
The Frontier in American History (1921, US) – Frederick Jackson Turner
Black Lamb and Grey Falcon: A Journey Through Yugoslavia (1941, UK) – Rebecca West
The Nature and Destiny of Man (1943, US) – Reinhold Niebuhr
The Hero With A Thousand Faces (1949, US) – Joseph Campbell
The Story of Art (1950, Austria/UK) – E. H. Gombrich
Notes of a Native Son (1955, US) – James Baldwin
The Sweet Science (1956, US) – A. J. Liebling
Night (1958, Romania/France/US) – Elie Wiesel
A Moveable Feast (c. 1960, pub. 1964, US) – Ernest Hemingway
The Death and Life of Great American Cities (1961, US) – Jane Jacobs
Mastering The Art of French Cooking (Vol. 1: 1961; Vol. 2: 1970, US/France) – Julia Child, with Simone Beck and Louisette Bertholle
The Making of the English Working Class (1963, UK) – E. P. Thompson
Why We Can’t Wait – (1964, US) Martin Luther King, Jr.
Understanding Media: The Extensions of Man (1964, Canada) – Marshall McLuhan
The Medium is the Massage: An Inventory of Effects (1967, Canada/UK) – Marshall McLuhan & Quentin Fiore
A Theory of Justice (1971, US) – John Rawls
Our Bodies, Ourselves (1971, US) – Boston Women’s Health Book Collective
Fear and Loathing in Las Vegas: A Savage Journey to the Heart of the American Dream (1972, US) – Hunter S. Thompson
The Joy of Sex (1972, UK) – Alex Comfort
Ways of Seeing (1972, UK) – John Berger
The Gulag Archipelago: 1918-1956 (1973, USSR) – Aleksandr Solzhenitsyn
Working (1974, US) – Studs Terkel
Pilgrim At Tinker Creek (1974, US) – Annie Dillard
The Lives of a Cell: Notes of a Biology Watcher (1974, US) – Lewis Thomas
Helter Skelter: the True Story of the Manson Murders (1974, US) – Vincent Bugliosi & Curt Gentry
The Power Broker: Robert Moses and the Fall of New York (1974, US) – Robert A. Caro
Discipline and Punish: The Birth of the Prison (1975, France) – Michel Foucault
The Executioner’s Song (1979, US) – Norman Mailer (also listed as fiction: novel)
Cosmos (1980, US) – Carl Sagan
The Making of the Atomic Bomb (1987, US) – Richard Rhodes
What It Takes: The Way to the White House (1992, US) – Richard Ben Cramer
The Hot Zone: The Terrifying True Story of the Origins of the Ebola Virus (1995, US) – Richard Preston
Into Thin Air: A Personal Account of the Mount Everest Disaster (1997, US) – Jon Krakauer
The Rape of Nanking: The Forgotten Holocaust of World War II (1997, US) – Iris Chang
No Logo: Taking Aim at the Brand Bullies (1999, Canada) – Naomi Klein
A Heartbreaking Work of Staggering Genius (2000, US) – Dave Eggers
The Tipping Point: How Little Things Can Make a Big Difference (2000, US) – Malcolm Gladwell
The Botany of Desire: A Plant’s-Eye View of the World (2001, US) – Michael Pollan
Salt: A World History (2002, US) – Mark Kurlansky
Under the Banner of Heaven: A Story of Violent Faith (2003, US) – Jon Krakauer
Stiff: The Curious Lives of Human Cadavers (2003, US) – Mary Roach
Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation (2003, UK) – Lynne Truss
Shadow Divers (2004, US) – Robert Kurson
The Year of Magical Thinking (2005, US) – Joan Didion
Postwar: A History of Europe since 1945 (2005, UK) – Tony Judt
1491: New Revelations of the Americas Before Columbus (2005, US) – Charles C. Mann
Freakonomics: A Rogue Economist Explores the Hidden Side of Everything (2005, US) – Steven D. Levitt
Mayflower: A Story of Courage, Community, and War (2006, US) – Nathaniel Philbrick
The Looming Tower: Al-Qaeda and the Road to 9/11 (2006, US) – Lawrence Wright
The Black Swan: The Impact of the Highly Improbable (2007, US) – Nassim Nicholas Taleb
The Last Lecture (2008, US) – Randy Pausch
Nothing to Envy: Ordinary Lives in North Korea (2009, US) – Barbara Demick
The Immortal Life of Henrietta Lacks (2010, US) – Rebecca Skloot
In the Garden of Beasts: Love, Terror, and an American Family in Hitler’s Berlin (2011, US) – Erik Larson
The Power of Habit: Why We Do What We Do in Life and Business (2012, US) – Charles Duhigg