What are they?

Mine Are:

William Hartnell
B: The Dalek Invasion Of Earth
W: The War Machines

Patrick Troughton
B: The Mind Robber
W: The Krotons

Jon Pertwee
B: The Curse Of Peladon
W: The Mutants

Tom Baker
B: Genesis Of The Daleks
W: The Leisure Hive

Peter Davison
B: The Five Doctors
W: Frontios

Colin Baker
B: Vengeance On Varos
W: Timelash

Sylvester McCoy
B: Ghost Light
W: Time and the Rani

Paul McGann
B: Movie
W: Movie

Chris Eccleston
B: Bad Wolf/Parting Of The Ways
W: Fathers Day

David Tennant
B: The Stolen Earth/Journeys End
W: The Fires Of Pompeii

Matt Smith
B: The Name Of The Doctor
W: The Girl Who Waited

OMG! Fathers Day, Fires of Pompeii (loved that one!!) and The Girl Who Waited were amazing!!.... !!!!!!!

Oh and you gotta love Let's Kill Hitler and Demon's Run! EPIC! "You've got a time machine, I've got a gun. What the hell, Let's kill Hitler!"

William Hartnell
B: The Aztecs
W: An Unearthly Child

Patrick Troughton
B: Tomb of the Cybermen
W: The Krotons

Jon Pertwee
B: The claws of Axos
W: Terror of the Autons

Tom Baker
B: Genesis Of The Daleks
W: Logopolis

Peter Davison
B: Resurrection of the Daleks
W: The Five Doctors

Colin Baker
B: Trial of a Timelord
W: The Two Doctors

Sylvester McCoy
B: Rememberance of the Daleks
W: Dragonfire

Paul McGann
B: Shada
W: The TV Movie

Chris Eccleston
B: The Empty Child/Doctor Dances
W: Aliens over London/WW3

David Tennant
B: Sound of Drums/Last of the timelod
W: Love and Monsters

Matt Smith
B: The Name Of The Doctor
W: Rings of Athaken

I haven't seen enough of Classic Who to complete a full list, but I'll do Nu'Who

The Ninth Doctor
Best: The Parting of the Ways
Second Best: The Empty Child
Worst: The Long Game

The Tenth Doctor
Best: The Stolen Earth
Second Best: Planet of the Ood
Worst: The End of Time: Part One

The Eleventh Doctor
Best: A Christmas Carol
Second Best: The Doctor's Wife
Worst: The Doctor, The Widow and the Wardrobe

I cant honestly say a single best or worst so I'll play the game like this: I'll say the first story that comes into my head for each category:

(best on top; worst below)

Hartnell:

The Aztecs
The Space Museum

Troughton:

Power of the Daleks
The Dominators

Pertwee:

Doctor Who and the Silurians
The Monster of Peladon

T.Baker:

City of Death
Robot

Davison:

Caves of Androzani
Time-flight

C. Baker:

Vengeance on Varos
The Twin Dilemma

McCoy:

Ghost Light
The Happiness Patrol

Ecclestone:

The Empty Child
Father's Day

Tennant:

Blink
The Fires of Pompeii

Smith:

The Name of the Doctor
A Town Called Mercy

Best
Worse

Hartnell:

The War Machines
The Ark


Troughton:

Tomb of he Cybermen
The Mind Robber


Pertwee:

Spearhead from Space
The Mutants


T.Baker:

Pyramids of Mars
Underworld


Davison:

Earthshock
Snakedance


C. Baker:

Mark of the Rani
The Twin Dilemma


McCoy:

Remembrance of the Daleks
Paradise Towers


Eccleston:

The Empty Child
The Long Game


Tennant:

Blink
Fear Her


Smith:

The Name of the Doctor
The Doctor, The Widow and the Wardrobe

William Hartnell
Best: The War Machines
Worst: The Space Museum

Patrick Troughton
Best: The Abominable Snowmen
Worst: The Space Pirates (least fave Classic Who story)

Jon Pertwee
Best: The Daemons
Worst: Colony In Space

Tom Baker
Best: The Deadly Assassin
Worst: Underworld

Peter Davison
Best: Mawdryn Undead
Worst: Frontios

Colin Baker
Best: Vengeance on Varos
Worst: Twin Dilemma

Sylvester McCoy
Best: Curse of Fenric
Worst: Time and the Rani

Paul McGann
Best: none
Worst: That movie

Christopher Ecclestone
Best: Empty Child
Worst: Aliens of London

David Tennant
Best: Blink
Worst: Love and Monsters

Matt Smith
Best: The Eleventh Hour
Worst: Cold Blood

Just about to start Pertwee's era tomorrow and watch it and the Baker era. So far, I've only watched The Fifth Doctor onwards.

Davison
Best: The Caves of Androzani
Worst: Four to Doomsday

Colin Baker
Best: Trial of a Time Lord- Terror of the Vervoids (loved that story; even Mel was bearable)
Worst: The Twin Dilemma (quite possibly the worst piece of drama I've ever watched)
Special mention to The Two Doctors which was also abysmal.

McCoy
Best: The Curse of Fenric
Worst: Delta and the Bannermen

McGann
His only TV Movie was a bit meh, but I wouldn't call it terrible. I'm intending to eventually listen to some of McGann's audio stories in the future so one of those is likely to be the best but also probably the worst.

Eccleston
Best: Dalek
Worst: Boom Town (still far from terrible)

Tennant
Best: Human Nature/Family of Blood
Worst: Love and Monsters

Smith
Best: Amy's Choice
Worst: The Doctor, the Widow and the Wardrobe (again, I wouldn't call it terrible, but still the worst)

I've only watched a handful of the classic Doctors stories so I'll just do those of the modern Doctors.

Christopher Ecclestone:
Best - Dalek
Worst - Aliens of London/World War Three

David Tennant:
Best - Turn Left
Worst - Love & Monsters

Matt Smith (so far):
Best - Cold War
Worst - The Doctor, The Widow and The Wardrobe.

I'm afraid that I can't comment on old who and seen very few episodes and most from the Tom Baker era so am only going to go from Eccleston (McGann only having the film not being worth it for him):

Christopher Eccleston:
Best:Unquiet Dead (The Empty Child/The Doctor Dances an extremely close second)
Worst: Aliens of London/World War 3

David Tennant:
Best: Blink (with out a shadow of a doubt)
Worst: Fear her (the worst Nu-who episode ever Love and Monsters is very close behind however)

Matt Smith:
Best: The Name of the Doctor
Worst: The Bells of Saint John

Hartnell:

Best-The Time Meddler
Worst-The Myth Makers

Troughton

Best-The Web Of Fear
Worst-The Space Pirates

Pertwee:

Best-The Three Doctors
Worst-The Silurians

Tom Baker:

Best-Logopolis
Worst-Underworld

Davison:

Best-The Caves Of Androzani
Worst-Terminus

Colin Baker:

Best-The Ultimate Foe(12-13 TOATL)
Worst-The Twin Dilemma

McCoy:

Best-Survival
Worst-Paradise Towers

McGann:

Movie was brilliant

Ecclestone:

Best-Bad Wolf/Parting Of The Ways
Worst-The Long Game

Tennant:

Best-Army Of Ghosts/Doomsday
Worst-Love And Monsters

Smith:

Best-Let's Kill Hitler
Worst- Rings Of Athaken

Eccleston
Best: Empty Child / The Doctor Dances (8/10)
Honorable mentions: The Unquiet Dead (8/10)
Worst: Boom Town (2/10)

Tennant
Best: Human Nature/Family of Blood (10+/10)
Honorable mentions: Silence in the Library / Forest of the Dead (10/10), Blink (10/10), Gridlock (10/10), Midnight (10/10), Planet of the Dead (10/10), Shakespeare Code (10/10) and Partners in Crime (10/10)
Worst: Love and Monsters (0/10) and Stolen Earth / Journey's End (0/10)

Smith
Best: The Snowmen (10+/10)
Honorable mentions: The Rings of Akhaten (10/10), Amy's Choice (10/10), Nightmare in Silver (10/10), Night Terrors (10/10), Hide (10/10), The God Complex (10/10) and Eleventh Hour (10/10)
Worst: Rebel Flesh / The Almost People (1/10)


* in honorable mentions I mentioned all episodes which are 10/10 (or 8/10 in Eccleston season)

* I haven't watched The name of the Doctor yet

William Hartnell
B: Marco Polo
W: The Chase

Patrick Troughton
B: The Web Of Fear
W: The Dominators

Jon Pertwee
B: Inferno
W: The Time Monster

Tom Baker
B: The Talons Of Weng Chiang
W: Meglos

Peter Davison
B: Kinda
W: The Kings Demons

Colin Baker
B: Revelation Of The Daleks
W: Attack Of The Cybermen

Sylvester McCoy
B: The Curse Of Fenric
W: Paradise Towers

Paul McGann
B: The TV Movie
W: The TV Movie

Chris Eccleston
B: The Empty Child/Doctor Dances
W: The Long Game

David Tennant
B: Turn Left
W: The Daleks Take Manhatten

Matt Smith
B: The Doctor's Wife
W: Let's Kill Hitler

William Hartnell
Best: The Aztecs
Worst: The Space Museum

Patrick Troughton
Best: Tomb of the Cybermen
Worst: The Krotons

Jon Pertwee
Best: The Daemons
Worst: The Mutants

Tom Baker
Best: Genesis of The Daleks
Worst: Underworld

Peter Davison
Best: The Caves of Androzani
Worst: Time Flight

Colin Baker
Best: Vengeance on Varos
Worst: Twin Dilemma

Sylvester McCoy
Best: Ghost Light
Worst: The Happiness Patrol

Christopher Eccleston
Best: Parting of The Ways / The Empty Child
Worst: The Long Game

David Tennant
Best: Human Nature / Family of Blood
Worst: Love and Monsters / Fear Her

Matt Smith
Best: The Eleventh Hour / Name of The Doctor
Worst: The Doctor, the Widow and the Wardrobe / The Hungry Earth

Hartnell:
Best. The Ark
Worst. The Daleks (I've surprised myself here)

Troughton:
B. The Tomb of the Cybermen
W. The Krotons

Pertwee:
B. The Claws of Axos
W. The Ambassors of Death

Tom Baker:
B. Genesis of the Daleks
W. Underworld

Davison:
B. Mawdryn Undead
W. Snakedance

Colin Baker:
B. Vengeance on Varos
W. The Twin Dilemma

McCoy:
B. Remembrance of the Daleks
W. The Happiness Patrol

McGann:
B/W. The Movie

Eccleston:
B. The Empty Child/The Doctor Dances
W. The Long Game

Tennant:
B. The Girl in the Fireplace
W. Love & Monsters/Fear Her (I hate these both equally)

Smith:
B. The Girl Who Waited
W. The Rings of Akhaten

Hartnell

B: Dalek Invasion of Earth
W: The Chase

Troughton

B: Tomb of the Cybermen
W: The Dominators

Pertwee

B: Inferno
W: The Monster of Peladon

T Baker

B: The Seeds of Doom
W: The Horns of Nimon

Davison

B: The Caves of Androzani
W: Terminus

C Baker

B: Revelation of the Daleks
W: The Twin Dilemma

McCoy

B: Rememberance of the Daleks
W: Time and the Rani

Eccleston

B: The Empty Child
W: World War Three

Tennant

B: Blink
W: Evolution of the Daleks

Smith

B: The Time of Angels
W: Lets Kill Hitler

William Hartnell
B: An Unearthly Child (Episode 1)
W: An Unearthly Child (Episodes 2, 3 and 4)

Patrick Troughton
B: The Mind Robber
W: The Krotons

Jon Pertwee
B: Carnival Of Monsters
W: Day Of The Daleks

Tom Baker
B: City Of Death
W: Nightmare Of Eden

Peter Davison
B: Enlightenment
W: Time-Flight

Colin Baker
B: Vengeance On Varos
W: The Twin Dilemma

Sylvester McCoy
B: Rememberance Of The Daleks
W: Time And The Rani

Paul McGann
B: TV Movie
W: TV Movie

Christopher Eccleston
B: The Empty Child / The Doctor Dances
W: Aliens Of London / World War Three

David Tennant
B: Blink
W: Fear Her

Matt Smith
B: The Impossible Astronaut / Day Of The Moon
W: Victory Of The Daleks

William Hartnell
B: The Romans
W: An Unearthly Child

Patrick Troughton
B: The Invasion
W: The Krotons

Jon Pertwee
B: Inferno
W: Death to the Daleks

Tom Baker
B: City of Death
W: Meglos

Peter Davison
B: Mawdryn Undead
W: Warriors of the Deep/Time Flight

Colin Baker
B: Revelation of the Daleks
W: The Twin Dilemma

Sylvester McCoy
B: Curse of Fenric
W: The rest (can't choose!)

Paul McGann
B/W: The TV Movie

Chris Eccleston
B: Parting of the Ways
W: Aliens of London/WW3

David Tennant
B: Utopia
W: Last of the Timelords

Matt Smith
B: The Name Of The Doctor
W: Victory of the Daleks

William Hartnell;
B: The Rescue
W: Planet of the Giants

Patrick Troughton;
B: The Mind Robber
W: The Dominators

Jon Pertwee;
B: Tie between Inferno and The Silurians (cheating!)
W: The Mutantzzzzz

Tom Baker;
B: Tough. Um...The Deadly Assassin (today)
W: Underworld

Peter Davison;
B: Enlightenment
W: Time-Flight

Colin Baker;
B: Revelation of the Daleks
W: Timelash

Sylvestor McCoy;
B: Greatest Show in the Galaxy
W: Time & The Rani

Christopher Eccleston;
B: Empty Child/Doctor Dances
W: Aliens of London/WW3

David Tennant;
B:Gridlock
W: Planet of the Dead

Matt Smith; (so far!)
B: The Doctor's Wife
W: Curse of the Black Spot

William Hartnell
B: The Aztecs
W: The Space Museum

Patrick Troughton
B: The Mind Robber
W: The Dominators

Jon Pertwee
B: Inferno
W: Planet of the Spiders

Tom Baker
B: Pyramids of Mars
W: The Invasion of Time

Peter Davison
B: The Caves of Androzani
W: Time Flight

Colin Baker
B: The Ultimate Foe (Part 1)
W: The Ultimate Foe (Part 2)

Sylvester McCoy
B: Dragonfire
W: Silver Nemesis

Paul McGann
B/W: The TV Movie

Chris Eccleston
B: The Empty Child/The Doctor Dances
W: Boom Town

David Tennant
B: The Waters of Mars
W: Voyage of the Damned

Matt Smith
B: The Name Of The Doctor
W: Victory of the Daleks

NuWho only:

Eccleston
Best: Dalek
Worst: Aliens of London/WW 3

Tennant
Best: Midnight
Worst: Idiot' Lantern

Smith
Best: The Name of the Doctor and The Big Bang (can't really decide)
Worst: Night Terrors

Hartnell
B: The Edge of Destruction
W: The Gunfighters

Troughton
B: The War Games (easily)
W: The Space Pirates

Pertwee
B: Inferno
W: The Monster of Peladon

T. Baker
B: Genesis of the Daleks
W: Underworld

Davison
B: The Caves of Androzani
W: Time-Flight

C. Baker
B: Mindwarp
W: The Twin Dilemma

McCoy
B: Remembrance of the Daleks
W: Time and the Rani

Eccleston
B: The Empty Child/The Doctor Dances
W: The Long Game

Tennant
B: Silence in the Library/Forest of the Dead
W: Fear Her

Smith
B: The Doctor's Wife
W: Night Terrors (without a shadow of a doubt)

I've only seen a couple of First and Second Doctor stories and probably around half of the Third Doctor's stories. I can only really start with the Fourth Doctor.

Tom Baker
Best: Pyramids of Mars
Worst: Revenge of the Cybermen

Peter Davison
Best: Kinda
Worst: Time Flight

Colin Baker
Best: Revelation of the Daleks
Worst: Twin Dilemma

Sylvester McCoy
Best: Remembrance of the Daleks
Worst: Time and the Rani

Christopher Eccleston
Best: The Empty Child/The Doctor Dances
Worst: Aliens of London/World War III

David Tennant
Best: Blink
Worst: Love and Monsters

Matt Smith
Best: Vincent and the Doctor
Worst: The Impossible Astronaut/Day of the Moon (and I'll shock you further, I think it's the worst ever)

Christopher Eccleston
B - The Empty Child/The Doctor Dances
W - The Long Game

David Tennant
B - Turn Left
W - Smith and Jones

Matt Smith
B - The Angels Take Manhattan
W - Dinosaurs on a Spaceship

William Hartnell (Haven't watched that much)
Best: The Aztecs
Worst: The Edge Of Destrusction
Patrick Troughton (Watched very little)
Best: The War Games
Worst: The Wheel In Space
Jon Pertwee
Best: Inferno
Worst: The Time Monster (But I Did Enjoy it)
Tom Baker
Best: The Seeds of Doom
Worst: The Armageddon Factor
Peter Davison
Best: The Caves of Androzani
Worst: Time Filght
Colin Baker
Best: Revelation of The Daleks
Worst: Timelash
Sylvester McCoy
Best:Remebrance of The Daleks
Worst: Haven't watched enough
Paul McGann
Best and Worst: The TV Movie
Christopher Eccleston
Best: The Empty Child/The Doctor Dances
Worst: The Long Game
David Tennant
Best: The Unicorn and The Wasp
Worst: Fear Her
Matt Smith
Best: Vincent and The Doctor
Worst: Let's Kill Hitler