I collected 10 lists of the Best Non-Fiction Books of All Time and combined them into one meta-list.  Here are the results: every non-fiction book on at least two of the original source lists, organized chronologically.  NOTE: These are not my personal opinions and I have not read all these books.

To see a version of this list organized by rank (that is, with the books on the most lists at the top), go here.

500 BCE – 1 BCE
The Histories (440 BCE, Ancient Greece) – Herodotus (on 3 lists)
The History of the Peloponnesian War (c. 431-410 BCE, Ancient Greece) – Thucydides (on 2 lists)
The Art of War (c. 499-400 BCE, China) – Sun Tzu (Sunzi) (attrib.) (on 2 lists)
The Republic (c. 380 BCE, Ancient Greece) – Plato (on 3 lists)
Symposium (c. 385-370 BCE, Ancient Greece) – Plato (on 2 lists)
The Analects (c. 475-221 BCE, China) – Confucius (attrib.) (on 2 lists)

1 CE- 1499 CE
Meditations (180 CE, Ancient Rome) – Marcus Aurelius (on 2 lists)
Confessions (c. 397-400 CE, Ancient Rome/Numidia) – Augustine of Hippo (on 2 lists)

1500-1799
The Prince (1532, Italy) – Niccolò Machiavelli (on 6 lists)
The Lives of the Most Excellent Painters, Sculptors, and Architects (1550, Italy) – Giorgio Vasari (on 2 lists)
Essays (1580, France) – Michel de Montaigne (on 3 lists)
Leviathan (1651, UK) – Thomas Hobbes (on 3 lists)
Philosophae Naturalis Principia Mathematica (1687, UK) – Isaac Newton (on 2 lists)
The Confessions (1769, pub. 1782, France/Switzerland) – Jean-Jacques Rousseau (on 2 lists)
The Wealth of Nations (1776, GB) – Adam Smith (on 2 lists)
Critique of Pure Reason (1781, Germany) – Immanuel Kant (on 2 lists)
The History of the Decline and Fall of the Roman Empire (1776-1789, GB) – Edward Gibbon (on 2 lists)
The Life of Samuel Johnson, LL.D. (1791, UK) – James Boswell (on 3 lists)
Rights of Man (1791 (Pt. 1); 1792 (Pt. 2), UK) – Thomas Paine (on 3 lists)
A Vindication of the Rights of Woman (1792, UK) – Mary Wollstonecraft (on 2 lists)

1800-1899
Democracy in America (1835 (Pt. 1), 1840 (Pt. 2), France) – Alexis de Tocqueville (on 3 lists)
Narrative of the Life of Frederick Douglass, an American Slave (1845, US) – Frederick Douglass (on 2 lists)
The Communist Manifesto (1848, UK) – Karl Marx & Friedrich Engels (on 4 lists)
Walden (1854, US) – Henry David Thoreau (on 4 lists)
On the Origin of Species (1859, UK) – Charles Darwin (on 6 lists)
On Liberty (1859, UK) – John Stuart Mill (on 3 lists)
Das Kapital: Critique of Political Economy (1867-1883, Germany/UK) – Karl Marx (on 2 lists)
The Golden Bough: A Study in Comparative Religion (1890, UK) – James George Frazer (on 2 lists)
Thus Spoke Zarathustra (1883-1891, Germany) – Friedrich Nietzsche (on 2 lists)
The Interpretation of Dreams (1899, Austria) – Sigmund Freud (on 4 lists)

1900-1949
Up From Slavery (1901, US) – Booker T. Washington (on 2 lists)
The Varieties of Religious Experience (1902, US) – William James (on 3 lists)
The Souls of Black Folk (1903, US) – W.E.B. Du Bois (on 2 lists)
Relativity: The Special and General Theory (1916, Germany) – Albert Einstein (on 2 lists)
The Elements of Style (1918, US) – William Strunk & E. B. White (on 6 lists)
Eminent Victorians (1918, US) – Lytton Strachey (on 3 lists)
The Frontier in American History (1921, US) – Frederick Jackson Turner (on 2 lists)
Seven Pillars of Wisdom: A Triumph (1922, pub. 1926, UK) – T. E. Lawrence (on 3 lists)
A Room of One’s Own (1929, UK) – Virginia Woolf (on 6 lists)
Goodbye To All That (1929, UK) – Robert Graves (on 4 lists)
The Autobiography of Alice B. Toklas (1933, US/France) – Gertrude Stein (on 3 lists)
The General Theory of Employment, Interest, and Money (1936, UK) – John Maynard Keynes (on 3 lists)
Out of Africa (1937, UK/Denmark) – Isak Dinesen (on 3 lists)
Homage To Catalonia (1938, UK) – George Orwell (on 6 lists)
Let Us Now Praise Famous Men (1941, US) – James Agee (text) & Walker Evans (photos) (on 3 lists)
Black Lamb and Grey Falcon: A Journey Through Yugoslavia (1941, UK) – Rebecca West (on 2 lists)
The Nature and Destiny of Man (1943, US) – Reinhold Niebuhr (on 2 lists)
Black Boy (1945, US) – Richard Wright (on 3 lists)
Hiroshima (1946, US) – John Hersey (on 4 lists)
The Diary of a Young Girl (1947, The Netherlands) – Anne Frank (on 6 lists)
The Second Sex (France, 1949) – Simone de Beauvoir (on 3 lists)
The Hero With A Thousand Faces (1949, US) – Joseph Campbell (on 2 lists)

1950-1974
The Story of Art (1950, Austria/UK) – E. H. Gombrich (on 2 lists)
Speak, Memory (1951, USSR/US) – Vladimir Nabokov (on 5 lists)
Notes of a Native Son (1955, US) – James Baldwin (on 2 lists)
The Sweet Science (1956, US) – A. J. Liebling (on 2 lists)
Mythologies (1957, France) – Roland Barthes (on 3 lists)
Night (1958, Romania/France/US) – Elie Wiesel (on 2 lists)
The Rise and Fall of The Third Reich: A History of Nazi Germany (1960, US) – William L. Shirer (on 3 lists)
A Moveable Feast (c. 1960, pub. 1964, US) – Ernest Hemingway (on 2 lists)
The Death and Life of Great American Cities (1961, US) – Jane Jacobs (on 2 lists)
Mastering The Art of French Cooking (Vol. 1: 1961; Vol. 2: 1970, US/France) – Julia Child, with Simone Beck and Louisette Bertholle (on 2 lists)
Silent Spring (1962, US) – Rachel Carson (on 8 lists)
The Structure of Scientific Revolutions (1962, US) – Thomas S. Kuhn (on 4 lists)
The Guns of August (1962, US) – Barbara Tuchman (on 3 lists)
The Feminine Mystique (1963, US) – Betty Friedan (on 3 lists)
The Making of the English Working Class (1963, UK) – E. P. Thompson (on 2 lists)
Why We Can’t Wait (1964, US) – Martin Luther King, Jr. (on 2 lists)
Understanding Media: The Extensions of Man (1964, Canada) – Marshall McLuhan (on 2 lists)
The Autobiography of Malcolm X (1965, US) – Malcolm X with Alex Haley (on 5 lists)
In Cold Blood (1966, US) – Truman Capote (on 8 lists)
The Medium is the Massage: An Inventory of Effects (1967, Canada/UK) – Marshall McLuhan & Quentin Fiore (on 2 lists)
The Double Helix: A Personal Account of the Discovery of the Structure of DNA (1968, US) – James D. Watson (on 4 lists)
Slouching Towards Bethlehem (1968, US) – Joan Didion (on 4 lists)
The Electric Kool-Aid Acid Test (1968, US) – Tom Wolfe (on 4 lists)
I Know Why The Caged Bird Sings (1969, US) – Maya Angelou (on 3 lists)
Bury My Heart At Wounded Knee (1970, US) – Dee Brown (on 6 lists)
A Theory of Justice (1971, US) – John Rawls (on 2 lists)
Our Bodies, Ourselves (1971, US) – Boston Women’s Health Book Collective (on 2 lists)
Fear and Loathing in Las Vegas: A Savage Journey to the Heart of the American Dream (1972, US) – Hunter S. Thompson (on 2 lists)
The Joy of Sex (1972, UK) – Alex Comfort (on 2 lists)
Ways of Seeing (1972, UK) – John Berger (on 2 lists)
The Gulag Archipelago: 1918-1956 (1973, USSR) – Aleksandr Solzhenitsyn (on 2 lists)
All The President’s Men (1974, US) – Carl Bernstein & Bob Woodward (on 4 lists)
The Civil War: A Narrative (1974, US) – Shelby Foote (on 3 lists)
Zen and The Art of Motorcycle Maintenance: An Inquiry Into Values (1974, US) – Robert M. Pirsig (on 3 lists)
Working (1974, US) – Studs Terkel (on 2 lists)
Pilgrim At Tinker Creek (1974, US) – Annie Dillard (on 2 lists)
The Lives of a Cell: Notes of a Biology Watcher (1974, US) – Lewis Thomas (on 2 lists)
Helter Skelter: the True Story of the Manson Murders (1974, US) – Vincent Bugliosi & Curt Gentry (on 2 lists)
The Power Broker: Robert Moses and the Fall of New York (1974, US) – Robert A. Caro (on 2 lists)

1975-1999
The Great War and Modern Memory (1975, US) – Paul Fussell (on 3 lists)
Discipline and Punish: The Birth of the Prison (1975, France) – Michel Foucault (on 2 lists)
The Selfish Gene (1976, UK) – Richard Dawkins (on 3 lists)
Dispatches (1977, US) – Michael Herr (on 4 lists)
Orientalism (1978, Palestine/US) – Edward W. Said (on 3 lists)
The Gnostic Gospels (1979, US) – Elaine Pagels (on 4 lists)
The Right Stuff (1979, US) – Tom Wolfe (on 4 lists)
Gödel, Escher, Bach: An Eternal Golden Braid (1979, US) – Douglas Hofstadter (on 3 lists)
The Executioner’s Song (1979, US) – Norman Mailer (also listed as fiction: novel) (on 2 lists)
A People’s History of the United States (1980, US) – Howard Zinn (on 3 lists)
Cosmos (1980, US) – Carl Sagan (on 2 lists)
Maus: A Survivor’s Tale: My Father Bleed’s History (1986, US) – Art Spiegelman (on 3 lists)
And The Band Played On: Politics, People, and The Aids Epidemic (1987, US) – Randy Shilts (on 3 lists)
The Making of the Atomic Bomb (1987, US) – Richard Rhodes (on 2 lists)
A Brief History of Time: From the Big Bang to Black Holes (1988, UK) – Stephen Hawking (on 5 lists)
The Journalist and The Murderer (1990, US) – Janet Malcolm (on 3 lists)
The Beauty Myth: How Images of Beauty Are Used Against Women (1990, US) – Naomi Wolf (on 3 lists)
What It Takes: The Way to the White House (1992, US) – Richard Ben Cramer (on 2 lists)
Midnight in the Garden of Good and Evil (1994, US) – John Berendt (on 3 lists)
The Hot Zone: The Terrifying True Story of the Origins of the Ebola Virus (1995, US) – Richard Preston (on 2 lists)
Into The Wild (1996, US) – Jon Krakauer (on 4 lists)
Guns, Germs, and Steel: The Fate of Human Societies (1997, US) – Jared Diamond (on 4 lists)
The Perfect Storm: A True Story of Men Against the Sea (1997, US) – Sebastian Junger (on 3 lists)
A Supposedly Fun Thing I’ll Never Do Again: Essays and Arguments (1997, US) – David Foster Wallace (on 3 lists)
Into Thin Air: A Personal Account of the Mount Everest Disaster (1997, US) – Jon Krakauer (on 2 lists)
The Rape of Nanking: The Forgotten Holocaust of World War II (1997, US) – Iris Chang (on 2 lists)
A Walk In The Woods: Rediscovering America on the Appalachian Trail (1998, US) – Bill Bryson (on 3 lists)
We Wish To Inform You That Tomorrow We Will Be Killed With Our Families: Stories from Rwanda (1998, US) – Philip Gourevitch (on 3 lists)
No Logo: Taking Aim at the Brand Bullies (1999, Canada) – Naomi Klein (on 2 lists)

2000-Present
On Writing: A Memoir of The Craft (2000, US) – Stephen King (on 4 lists)
A Heartbreaking Work of Staggering Genius (2000, US) – Dave Eggers (on 2 lists)
The Tipping Point: How Little Things Can Make a Big Difference (2000, US) – Malcolm Gladwell (on 2 lists)
Fast Food Nation: The Dark Side of The All-American Meal (2001, US) – Eric Schlosser (on 4 lists)
Nickel and Dimed: On (Not) Getting By In America (2001, US) – Barbara Ehrenreich (on 4 lists)
The Botany of Desire: A Plant’s-Eye View of the World (2001, US) – Michael Pollan (on 2 lists)
Salt: A World History (2002, US) – Mark Kurlansky (on 2 lists)
The Devil in the White City: Murder, Magic, and Madness at the Fair That Changed America (2003, US) – Erik Larson (on 4 lists)
Moneyball: The Art of Winning an Unfair Game (2003, US) – Michael Lewis (on 3 lists)
Under the Banner of Heaven: A Story of Violent Faith (2003, US) – Jon Krakauer (on 2 lists)
Stiff: The Curious Lives of Human Cadavers (2003, US) – Mary Roach (on 2 lists)
Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation (2003, UK) – Lynne Truss (on 2 lists)
Shadow Divers (2004, US) – Robert Kurson (on 2 lists)
The Year of Magical Thinking (2005, US) – Joan Didion (on 2 lists)
Postwar: A History of Europe since 1945 (2005, UK) – Tony Judt (on 2 lists)
1491: New Revelations of the Americas Before Columbus (2005, US) – Charles C. Mann (on 2 lists)
Freakonomics: A Rogue Economist Explores the Hidden Side of Everything (2005, US) – Steven D. Levitt (on 2 lists)
Mayflower: A Story of Courage, Community, and War (2006, US) – Nathaniel Philbrick (on 2 lists)
The Omnivore’s Dilemma: A Natural History of Four Meals (2006, US) – Michael Pollan (on 3 lists)
The Looming Tower: Al-Qaeda and the Road to 9/11 (2006, US) – Lawrence Wright (on 2 lists)
The Black Swan: The Impact of the Highly Improbable (2007, US) – Nassim Nicholas Taleb (on 2 lists)
Outliers: The Story of Success (2008, US) – Malcolm Gladwell (on 3 lists)
The Last Lecture (2008, US) – Randy Pausch (on 2 lists)
The Lost City of Z: A Tale of Deadly Obsession in the Amazon (2009, US) – David Grann (on 3 lists)
Nothing to Envy: Ordinary Lives in North Korea (2009, US) – Barbara Demick (on 2 lists)
The Emperor of All Maladies: A Biography of Cancer (2010, US) – Siddhartha Mukherjee (on 4 lists)
The Immortal Life of Henrietta Lacks (2010, US) – Rebecca Skloot (on 2 lists)
In the Garden of Beasts: Love, Terror, and an American Family in Hitler’s Berlin (2011, US) – Erik Larson (on 2 lists)
The Power of Habit: Why We Do What We Do in Life and Business (2012, US) – Charles Duhigg (on 2 lists)