Mine Are:

First Doctor

1. The Dalek Invasion of Earth
2. The Reign of Terror

Second Doctor

1. The Tomb of the Cybermen
2. The Krotons

Third Doctor

1. The Time Warrior
2. The Mutants

Fourth Doctor

1. Destiny of the Daleks
2. The Sun Makers

Fifth Doctor

1. Ressurection of the Daleks
2. Four to Doomsday

Sixth Doctor

1. Mark of the Rani
2. Pretty much all of Trial of a Timelord

Seventh Doctor

1. Remembrance of the Daleks
2. Survival

Ninth Doctor (Not counting McGann, as there was only one)

1. Aliens of London/World War Three
2. Boom Town

Tenth Doctor

1. The Stolen Earth/Journey's End
2. Fear Her (Midnight comes a close second)

Eleventh Doctor

1. Time of Angels/Flesh and Stone
2. The God Complex

I can only comment from Nine onwards:

Christopher Ecclestone:
Best - The Parting of the Ways
Worst - The Long Game

David Tennant:
Best - Doomsday
Worst - Love & Monsters

Matt Smith:
Best - The Name of the Doctor
Worst - The Lodger

I've noticed a pattern, my favourites are all finales, while my least favourites are all also from the same general area in the latter part of the series.

Nine
Best: The Parting of the Ways
Worst: World War Three

Ten
Best: Doomsday
Worst: The Waters of Mars

Eleven
Best: The Big Bang
Worst: The Rings of Akhaten

Best
Worst

Hartnell:
The Time Meddler
The Web Planet

Troughton:
The Invasion
The Krotons

Pertwee:
Spearhead from Space
The Time Monster (cure for insomnia)

Tom Baker:
The Robots of Death (Favourite Classic Series)
Underworld

Davison:
The Caves of Androzani
Planet of Fire

Colin Baker:
Attack of the Cybermen
Mindwarp

McCoy:
Remembrance of the Daleks
Time and the Rani

McGann:
ahem...The Movie

Ecclestone:
Bad Wolf/The Parting of the Ways
Boom Town (still not a bad story though)

Tennant:
Human Nature/The Family of Blood (Doomsday on another day!)
Fear Her

Smith:
The Name of the Doctor (favourite new dr who)
A Christmas Carol

Hartnell:

Best, The Massacre of St Bartholomew's Eve
Worst, The Celestial Toymaker

Troughton

Best, The Invasion
Worst, The Krotons

Pertwee

Best, The Daemons
Worst, Colony in Space

Tom Baker

Best, Terror of the Zygons, tempted to put Horns of Nimon though.
Worst, Underworld

Davison

Best, The Caves of Androzani
Worst, Warriors of the Deep

THE Colin Baker

Best, Revelation of the Daleks
Worst, The Twin Dilemma

McCoy

Best, Survival
Worst, Silver Nemesis

Eccleston

Best, Empty Child/The Doctor Dances
Worst, The Long Game

Tennant

Best, Utopia
Worst, Voyage of the Damned

Smith

Best, Asylum of the Daleks
Worst, Victory of the Daleks

Hartnell

The Romans/The Gunfighters
The Web Planet

Troughton

The War Games
The Dominators

Pertwee

The Mind of Evil
The Mutants

T Baker

The Talons of Weng Chiang
Underworld

Davison

The Caves of Androzani
Terminus

C Baker

Mind Warp
The Twin Dilemma

Mccoy

The Happiness Patrol
Time and the Rani

Nine
Best: Dalek
Worst: The Unquiet Dead

Ten
Best: Utopia
Worst: 42

Eleven
Best: The Name of The Doctor
Worst: The Rings of Akhaten/The Doctor, the Widow and the Wardrobe

William Hartnell
Best - The Dalek Invasion of Earth
Worst - The Web Planet
Patrick Troughton
Best - The Invasion
Worst - The Krotons
Jon Pertwee
Best - The Daemons
Worst - The Monster of Peladon
Tom Baker
Best - Terror of the Zygons
Worst - Underworld
Peter Davison
Best - Caves of Andozani
Worst - Warriors of the Deep
Colin Baker
Best - Vengence On Varos
Worst - Mark of the Rani
Sylvester McCoy
Best - The Happiness Patrol
Worst - Battlefield
Paul McGann
Best - the TV film
Worst - the TV film
Christopher Eccleston
Best - Empty Child/Doctor Dances
Worst - Aliens of London/World War three
David Tennant
Best - Human Nature/Family of Blood
Worst - Fear Her
Matt Smith
Best- The Doctor's Wife
Worst - The Curse of the Black Spot

William Hartnell
Best: The Ark
Worst: The Daleks (I find it boring)

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

Jon Pertwee
B: The Claws of Axos
W: The Ambassadors of Death

Tom Baker
B: Genesis of the Daleks
W: Underworld

Peter Davison
B: Mawdryn Undead
W: Kinda

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

Sylvester McCoy
B: Remembrance of the Daleks
W: Time And the Rani

Paul McGann
B: The Movie
W: The Movie

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

David Tennant
B: Silence in the Library/ Forest of the Dead
W: Love & Monsters

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

9 Best Dalek
Worst World War Three

10 Best Human Nature/Family of Blod
Worst Love and Monsters

11 Best AGMGTW
Worst Night Terrors

best story -wh-?,bad story-?
best story-pt war games worst story -?
best story -jp daemons worst the spider one (hate them)
best story-tb keeper of traken worst-genesis of daleks zzzzzzz
best story pd-the one where they go to the 1920s worst -the one where the dr has to regenarate after saving peri
colin baker-best-what was best ? worst-all sorry nice man but hee got some rotters
smcoy-best the one where ace sees her mum from the past
worst -the one with the bassetts monster
paul mcgann-didnt get a chance really only on big finish
c eccleston-best rose worst -the one with jack harkness meets rose eek
dt best -runaway bride v funny worst-unicorn and the wasp ??? agatha christie was an older lady , just didnt work

Matt smith-best-a christmas carol delightful xmas treat after the c""p of ee worst -the vampires in venice ??? what the ?

best dr -dt , worst sorry colin baker
ax

deleted

<deleted>

William Hartnell

Best: The Time Meddler
Worst: The Chase

Patrick Troughton

Best: The Tomb of the Cybermen
Worst: The Space Pirates

Jon Pertwee

Best: Carnival of Monsters
Worst: Death to the Daleks

Tom Baker

Best: Pyramids of Mars
Worst: Power of Kroll

Peter Davison

Best: Enlightenment
Worst: Time-Flight

Colin Baker

Best: Vengeance on Varos (at a push)
Worst: The Twin Dilemma

Sylvester McCoy

Best: The Curse of Fenric (at a push)
Worst: The Happiness Patrol

Paul McGann

...

Christopher Eccleston

Best: Father's Day
Worst: Aliens of London/World War Three

David Tennant

Best: The Girl in the Fireplace
Worst: Fear Her

Matt Smith

Best: Amy's Choice
Worst: The Doctor, the Widow and the Wardrobe.

Best = Worst Part 2

Eccleston

Fathers Day
The End of the World

Tennant

The Girl in the Fireplace/ Blink/ Human Nature/Family of Blood
The Doctors Daughter

Matt Smith ( so far)

A Christmas Carol
The Crimson Horror

Least Favorite Stories

First Doctor: The Mythmakers: I think it has to do more with the fact the story is mostly missing, and I only had audio to listen to. Without actually seeing what is going on, it can be a bit easy to lose track on what is happening.

Second Doctor: The Space Pirates: Same as above.

Third Doctor: The Ambassadors of Death: The story never really seemed to grip me too well.

Fourth: The Seeds of Doom: I felt it dragged on a bit for my tastes.

Fifth: Black Orchid: It was a bit weak compared to some of the other stories of that season.

Sixth: Time-Lash. I sort of forget a few things about it.

Seventh: Silver Nemesis: It's supposed to be the 25th anniversary special, but it doesn't feel too special. I also don't care for the the shiny Cybermen.

Eighth: Movie: It had it's moments...

Ninth: The Long Game: It sort of feels like RTD just wanted to glorify Rose even more.

Tenth: The Stolen Earth/Journey's End: The one story I simply can't stand to watch. I hate it, and it makes me angry.

Eleventh: The Beast Below: An okay story, but nothing too special.

Favorites:

First: The Celestial Toymaker: I love the premise behind the Toymaker, and I love how One goes one-on-one against him.

Two: The Mind Robber: It's very trippy, and it's difficult to really know what was going to happen next.

Three: Claw of Axos: The Axos are my absolute favorite Classic monster.

Fourth: Auntie Matter: I love how Four and Romana each stop the villain, both unaware of the other's involvement.

Fifth: The Kingmaker: I love Peri and Erimem's interactions in the story, as well as the villains. It also has a good deal of humor that cracks me up.

Sixth: The Holy Terror: It starts of really funny, and then gets really, really dark. It has one of my favorite endings to any story.

Seventh: Night Thoughts: Very chilling, and creepy and numerous times. "Mother's dead. Father's dead. They think your sisters drowned!"

Eighth: Lucie Miller/To The Death: In my opinion, the best Dalek story ever written. It blows everything RTD did out of the water.

Ninth: The Empty Child/The Doctor Dances: Moffat has said that "The Holy Terror" was his favorite Six story, and I can see that in this story, and I just love it.

Tenth: Blink: I love it when time travel is used in plots.

Eleventh: The Name of the Doctor: I love all those Classic clips show up, as well as the hints towards the Doctor's future.

The Seeds of Doom?!?!?! Worst place?!?!?!

So your saying the Seeds of Doom is worse than the likes of Underworld, The Armageddon Factor and The Creature from the Pit?!?!?!

The Seeds of Doom doesn't hardly have a resting moment in it so it can't have dragged on. You mustn't have been concentrating. Please watch it again.

It takes all sorts a couple posts above someone picked Genesis of the Daleks!
I think anyone who doesn't pick Underworld, hasn't seen it.

William Hartnell
B: An Unearthly Child
W: The Chase

Patrick Troughton
B: The Invasion
W: The Seeds of Death

Jon Pertwee
B: Planet of the Daleks
W: Frontier in Space

Tom Baker
B: Deadly Assassin
W: Revenge of the Cybermen

Peter Davison
B: Earthshock
W: Time-Flight

Colin Baker
B: Vengeance On Varos
W: Twin Dilema

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

Paul McGann
B: The Silver Turk (audio)
W: Movie

Chris Eccleston
B: Dalek
W: Boom Town

David Tennant
B: Midnight
W: Love and Monsters

Matt Smith
B: The Doctor's Wife
W: Rings of Akhaten

You missed eight Doctors!

your insane! and Colin had three great stories, Vengance on Varos, The Mark of the Rani and Trial of a Timelord (most of it anyway)

blasphemy!!!!!!!!

William Hartnell:
B: An Unearthly Child (Ep 1 only, I view it as separate to Eps 2-4, which I call 100,000BC,)
W: 100,000BC

Patrick Troughton:
B: The Invasion, W: The Dominators
May be changed on Nov 25th and Feb 24th

Jon Pertwee:
B: The Ambassadors of Death, W: Death to the Daleks

Tom Baker:
B: Terror of the Zygons, W: The Horns of Nimon

Peter Davison:
B: The Caves of Androzani, W: The King's Demons

Colin Baker:
B: Attack of the Cybermen, W: The Ultimate Foe

Sylvester McCoy:
B: The Greatest Show in the Galaxy, W: Delta and the Bannermen

Paul McGann:
B and W: The Movie
Not really fair, but hopefully this will change soon as I plan to start getting some 8th Doctor Big Finish after the New Year.

Christopher Eccleston:
B: Dalek, W: Aliens of London/World War Three

David Tennant:
B: The Waters of Mars, W: Love and Monsters

Matt Smith:
B: The Doctor's Wife, W: The Rings of Akhaten
May be changed after Nov 23rd and Dec 25th.

That's a little weird don't know how you can think that as they released them as the same story in multiple mediums, but each to there own

True, but the first episode is rather distinct from the others. The first episode is our introduction to the Doctor; the caveman story doesn't begin until part 2.