Exact Science
[Physics]
Absolute Zero - BBC (serie, 2 episodes)
Light Fantastic - BBC (serie, 4 episodes)
Atom - BBC (serie, 3 episodes)
Time - BBC (serie, 4 episodes)
Invisible Worlds - BBC (serie, 3 episodes)
Shock and Awe - BBC (serie, 3 episodes)
Everything and Nothing - BBC (serie, 2 episodes)
Order and Disorder - BBC (serie, 2 episodes)
The Fabric of the Cosmos - PBS (serie, 4 episodes)
Elegant Universe - PBS NOVA (serie, 3 episodes)
The Secret Life of Chaos - BBC
The Big Bang Machine - BBC
Feynman: Fun to Imagine - BBC
The Six Billion Dollar Experiment - BBC Horizon
Do You Know What Time it is? - BBC Horizon
How Long is a Piece of String? - BBC Horizon
What is Reality? - BBC Horizon
What is One Degree? - BBC Horizon
To Infinity and Beyond - BBC Horizon
What Happened Before the Big Bang - BBC Horizon
What on Earth is wrong with Gravity - BBC Horizon
Is Everything we Know about the Universe Wrong? - BBC Horizon
The End of God - BBC Horizon
Parallel Universes - BBC Horizon
Molecules with Sunglasses - BBC Horizon
Nanotopia - BBC Horizon
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[Biology]
The Shape of Life - PBS NOVA (serie, 8 episodes)
Evolution - PBS NOVA (serie, 7 episodes)
How to Grow a Planet - BBC (serie, 3 episodes)
Becoming Human - PBS NOVA (serie, 3 episodes)
The Origins of Us - BBC (serie, 3 episodes)
Inside the Human Body (serie, 4 episodes)
Into the Mind - BBC (serie, 3 episodes)
Superhuman - BBC (serie, 6 episodes)
Brain Story - BBC (serie, 6 episodes)
The Brain: A Secret History - BBC (serie, 3 episodes)
Human Sensens - BBC (serie, 3 episodes)
How to Build a Human - BBC (serie, 4 episodes)
First Life - BBC (serie, 2 episodes)
Wonders of Life - BBC (serie, 5 episodes)
The Secrets of the Mind - PBS NOVA
The Ghost in Your Genes - BBC Horizon
Fix Me - BBC Horizon
How Does Your Memory Work - BBC Horizon
Mad but Glad - BBC Horizon
Don't Grow Old - BBC Horizon
Are We Still Evolving? - BBC Horizon
The Secret You - BBC Horizon
The Secret Life of your Body Clock - BBC Horizon
.
[Geology]
Time Machine - BBC (serie, 3 episodes)
Earth, the Power of the Planet - BBC (serie, 5 episodes)
Journeys from the Center of the Earth - BBC (serie, 6 episodes)
Earth Story - BBC (serie, 8 episodes)
Journeys into the Ring of Fire (serie, 4 episodes)
The Beauty of Maps - BBC (serie, 4 episodes)
How the Earth Was Made - History Channel (serie, 2 seasons)
Cloudspotting - BBC
Snowball Earth - BBC Horizon
The Core - BBC Horizon
IMAX - Journey to Amazing Caves (docu-film)
.
[Astronomy]
The Planets - BBC (serie, 8 episodes)
Stephen Hawking's Universe - Discovery (serie, 6 episodes)
Into the Universe with Stephen Hawking - Discovery (serie, 3 episodes)
How the Universe Works - Discovery (serie, 8 episodes)
The Universe - History Channel (serie, 5 seasons)
Known Universe - NGC (serie, 6 episodes)
Wonders of the Solar System - BBC (serie, 5 episodes)
Wonders of the Universe - BBC (serie, 4 episodes)
Space - BBC (serie, 6 episodes)
The Search For Life: The Drake Equation - BBC
Titan A Place Like Home - BBC Horizon
Bye Bye Planet Pluto - BBC Horizon
The Death Star - BBC Horizon
The Hawking Paradox - BBC Horizon
Titan, A Place Like Home? - BBC Horizon
Supermassive Blackholes - BBC Horizon
Seeing Stars - BBC Horizon
Death Of The Universe - NGC
Origins - PBS Nova (serie, 4 episodes)
Welcome To Mars - PBS Nova
Voyage To The Mystery Moon - PBS Nova
Journey to the Edge of the Universe - NGC (docu-film)
IMAX - Space Station (docu-film)
IMAX - Hubble (docu-film)
.
[Nature]
Private Life of Plants - BBC (serie, 6 episodes)
Life in the Undergrowth - BBC (serie, 5 episodes)
Nature's Great Events - BBC (serie, 6 episodes)
Frozen Planet - BBC (serie, 7 episodes)
The Blue Planet - BBC (serie, 8 episodes)
Planet Earth - BBC (serie, 11 episodes)
Human Planet - BBC (serie, 8 episodes)
EarthFlight - BBC (serie, 6 episodes)
Great Barrier Reef - BBC (serie, 3 episodes)
Madagascar - BBC (serie, 3 episodes)
Galápagos - BBC (serie, 3 episodes)
Yellowstone - BBC (serie, 3 episodes)
Wild China - BBC (serie, 6 episodes)
Wild Pacific - BBC (serie, 5 episodes)
Ganges - BBC (serie, 3 episodes)
Africa - BBC (serie, 6 episodes)
Life - BBC (serie, 10 episodes)
Life on Earth - BBC (serie, 13 episodes)
The Living Planet - BBC (serie, 12 episodes)
The Trials of Life - BBC (serie, 12 episodes)
Life in the Freezer - BBC (serie, 6 episodes)
The Life of Birds - BBC (serie, 10 episodes)
The Life of Mammals - BBC (serie, 10 episodes)
Life in Cold Blood - BBC (serie, 5 episodes)
Wild Sex - NGC (serie, 6 episodes)
March of the Penguins (docu-film)
.
[Mixed]
The Ascent of Man - BBC (serie, 10 episodes)
Cosmos: A Personal Voyage - PBS (serie, 14 episodes)
The Day the Universe Changed - BBC (serie, 10 episodes)
The Story of Science: Power, Proof and Passion - BBC (serie, 6 episodes)
The Human Animal - BBC (serie, 6 episodes)
The Incredible Human Journey - BBC (serie, 5 episodes)
How Earth Made Us - BBC (serie, 5 episodes)
Chemistry, a Volatile History - BBC (serie, 3 episodes)
The Story of Maths - BBC (serie, 4 episodes)
The Code - BBC (serie, 3 episodes)
Visions of the Future - BBC (serie, 3 episodes)
Connections - BBC (serie, 3 seasons)
Swarm - BBC (serie, 2 episodes)
Dara Ó Briain's Science Club - BBC (serie, 6 episodes)
Brave New World - Channel 4 (serie, 5 episodes)
Through the Wormhole - Discovery (serie, 4 seasons)
Sci Fi Science: Physics of the Impossible - Discovery (serie, 2 seasons)
NatureTech (serie, 3 episodes)
The Pleasure of Finding Things Out (Richard Feynman)
Explosions, How we Shook the World - BBC
Afterlife: The Strange Science of Decay - BBC
The Voice - BBC
The Satellite Story - BBC
The Story of One - BBC
Do You See What I See? - BBC Horizon
The Lost World of Lake Vostok - BBC Horizon
Human v2.0 - BBC Horizon
Moon for Sale - BBC Horizon
Alien Planet - Discovery (docu-film)
Home (docu-film)
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Humanities
[War]
The World at War - (serie, 26 episodes)
Weird Weapons - History Channel (serie, 2 episodes)
Atlantic convoys - War at Sea (serie, 4 episodes)
Apocalypse: The Second World War (serie, 6 episodes)
Last Voices of WWI - History Channel (serie, 6 episodes)
Hitler's Warriors (serie, 6 episodes)
Fog of War (docu-film)
Nuit et brouillard - Night and Fog (docu-short)
Hearts and Minds (docu-film)
Restrepo (docu-film)
Armadillo (docu-film)
Trinity and Beyond (docu-film)
.
[Prehistory & earlier]
Walking with Sea Monsters - BBC (serie, 3 episodes)
Walking with Monsters - BBC (serie, 3 episodes)
Walking with Dinosaurs - BBC (serie, 6 episodes)
Walking with Beasts - BBC (serie, 6 episodes)
Walking with Cavemen - BBC (serie, 4 episodes)
The Mystery Of The Jurassic - BBC Horizon
Stone Age Columbus - BBC Horizon
The Day The Earth Almost Died - BBC Horizon
.
[Politics & Economics]
Commanding Heights - PBS NOVA (serie, 3 episodes)
The Ascent of Money - (serie, 6 episodes)
How Britain Made the Modern World - (serie, 6 episodes)
In Europa (serie, 30 episodes)
The Love of Money - BBC
Manufacturing Consent - Noam Chomsky (docu-film)
Rebel with a Pause - Noam Chomsky (docu-film)
The Shock doctrine - Naomi Klein (docu-film)
Promises (docu-film)
Inside Job (docu-film)
Chavez: Inside the Coup (docu-film)
The two Escobars (docu-film)
Taxi to the dark side (docu-film)
Taking liberties (docu-film)
The war on democracy (docu-film)
Gasland (docu-film)
Crude (docu-film)
Globalization is Good (docu-film)
The Corporation (docu-film)
Wal-mart: the High Cost of Low Price (docu-film)
Enron: the Smartest Guys in the Room (docu-film)
.
[Mixed subject]
The Virtual Revolution - BBC (serie, 4 episodes)
Civilization - BBC (serie, 13 episodes)
Science and Islam - BBC (serie, 3 episodes)
Fry's Planet Word - BBC (serie, 6 episodes)
Human, All Too Human - BBC (serie, 3 episodes)
The NASA Missions : When We Left Earth - Discovery (serie, 6 episodes)
Louis Theroux's Weird Weekends - (serie, 3 seasons)
When Louis Met... - (serie, 2 seasons)
Up - (serie, 7 docu-films)
The Boy With the Incredible Brain
The Century of the Self (serie, 4 episodes)
Woodstock (docu-film)
Grizzly Man (docu-film)
The King of Kong: A Fistful of Quarters (docu-film)
Defamation (docu-film)
Transcendent Man (docu-film)
We Live in Public (docu-film)
Friends of Kim (docu-film)
Lake of Fire (docu-film)
Into Eternity (docu-film)
The Machine That Made Us - BBC
James May On The Moon - BBC
Is Alcohol Worse than Ecstacy - BBC Horizon
A War On Science: Intelligent Design - BBC Horizon
All Watched over by Machines of Loving Grace - BBC (serie, 3 episodes)
.
[Special cases]
Koyaanisqatsi (docu-film)
Powaqqatsi (docu-film)
Naqoyqatsi (docu-film)
Chronos (docu-film)
Baraka (docu-film)
Samsara (docu-film)
51 Birch Street (docu-film)
Our Daily Bread (docu-film)
Rivers and Tides (docu-film)
Dark Side of the Moon (docu-film, don't research it (spoilers!) just watch!)
I'd also like to stress that BBC Horizon, now into its 49th season is prolly the best docu series of all time. You could include every single episode.