I've put together (just for this thread) a list of my favourite stories out of those I've seen...
One
An Unearthly Child [episode one]
The Daleks
The Aztecs
The Rescue
The Romans
The Chase
The Time Meddler
The War Machines
Two
The Tomb of the Cybermen
The War Games
Three
Doctor Who and the Silurians
The Curse of Peladon
The Sea Devils
The Green Death
Four
The Ark in Space
The Sontaran Experiment
Genesis of the Daleks
Revenge of the Cybermen
The Brain of Morbius
The Deadly Assassin
Destiny of the Daleks
Logopolis
Five
Mawdryn Undead
The Five Doctors
Six
Attack of the Cybermen
Revelation of the Daleks
TTOATL: The Mysterious Planet
TTOATL: The Ultimate Foe
Seven
Remembrance of the Daleks
The Curse of Fenric
Nine
The End of the World
Dalek
The Empty Child/The Doctor Dances
Ten
The Christmas Invasion
School Reunion
The Idiot's Lantern
The Impossible Planet/The Satan Pit
Army of Ghosts/Doomsday
The Runaway Bride
Smith and Jones
Gridlock
Human Nature/The Family of Blood
Blink
Utopia (but not the fuck-awful episodes that followed)
Time Crash
Partners in Crime
The Fires of Pompeii
Turn Left
The Stolen Earth/Journey's End
The Waters of Mars
The End of Time (quite iffy... only just makes the list)
Eleven
The Eleventh Hour
Victory of the Daleks
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