Best
1)The Deadly Assassin
2)City of Death
3)Genesis of the Daleks
4)Talons of Weng-Chiang
5)The Robots of Death

Worst
1)Underworld(worst)
2)The Invisible Enemy
3)The Invasion of Time
4)Meglos
5)Horns of Nimon

Interesting list - within your 'Best' section, numbers 2 to 5 all featured in the Top 10 most popular stories of all time (with "Genesis"... ranking at No. 1)
as voted for by readers of "Doctor Who Magazine" in a poll cast in 1998 - but from your 'Worst' section, only "Underworld" is in the Bottom 10!

Since I still have not seen of all classic Who, I can only say the best Tom Baker story was "City Of Death"
while his weakest ('worst' is too harsh a word) is "Meglos", for one plot element being repeated so often!

Underworld was pretty dull, bad CSO as I recall. Even Tom Baker couldn't save that story.

Best: City of Death
The Deadly Assassin
The Masque of Mandragora
Full Circle

Worst:

Creature from the Pit
The Android Invasion
The Horns of Nimon

Best

Terror of the Zygons
Genesis of the Daleks
Stones of Blood
Talons of Weng Chiang
Planet of Evil
Brain of Morbius

Worst

Logopolis
All the E Space stories
Horns of Nimon
The Deadly Assassin (controversial, but I find it so boring)

I'm not entirely sure I understand the concept of a 'worst' Tom Baker story. Surely Tom's presence guarantees that any story will be at the very least entertaining?

However, I'll make a stab at it...

Best:

1) Horror of Fang Rock
2) Terror of the Zygons
3) Talons of Weng Chiang
4) Pyramids of Mars
5) Warrior's Gate

Worst:

1) Underworld
2) The Sunmakers
3) The Invisible Enemy
4) Meglos
5) The Sontaran Experiment

Though I would place all of Tom's other stories far nearer to best than worst, and could easily have turned the top five into a top ten by adding City of Death, Robots of Death, Ark in Space, Brain of Morbius and Seeds of Doom.

One story that has not been listed by anyone is thread...is Tom Baker's debut "Robot".

And surely someone is willing to list "Shada" - even though it was never completed or broadcast!

Are you sure? Why??

In the case of the latter story, Baker should definitely have quit the role of The Doctor before his final season.
Interesting that his one of his best stories (the former) was from the season directly before!

That's because it's not good enough to be on anyone's 'best' list and not bad enough to be on anyone's 'worst', I think.

The former is from Tom Baker's penultimate season as The Doctor -
and the latter closed it, after "Shada" got disrupted by a strike.

Best:
1. Meglos
2. Meglos
3. Meglos
4. Meglos
5. Meglos

Worst:
1. Everything else



Just kidding! Even I don't like Meglos very much.
Best:
1. Talons of Weng Chiang
2. Deadly Assassin
3. City of Death
4. Stones of Blood
5. Horror of Fang Rock

(a few that missed out - Robots of Death, Warriors' Gate, Pyramids of Mars, Logopolis)

Worst:
1. Nightmare of Eden
2. Underworld
3. Creature from the Pit
4. Full Circle
5. The Invisible Enemy

Yes I am sure. However, I do echo ting in that I don't find any Tom Baker story that bad, given he is present in them.

Regarding Logopolis, its not a bad story or concept, but I have never really enjoyed it that much. I can't really pin-point why, but it is one of the stories I find a slog to get through.

Plus, until the dawn of Youtube, only those who paid loadsamoney for it on E-Bay could see it - correct?

Okay, this is hard but here goes......

Top 5

1)Logopolis
2)Pyramids Of Mars
3)City Of Death
4)The Sontaran Experiment
5)The Brain Of Morbius

Bottom 5

1)Revenge Of The Cybermen
2)Warriors Gate
3)The Ribos Operation
4)Underworld
5)The Talons Of Weng-Chiang

Okay, before everyone starts jumping to the defence of Talons Of Weng-Chiang, I acknowledge that it is a good story but I don't like historical stories that much, and there's something about it I don't like; I sometimes find hard to put a finger on it what it is. There's something about the whole period towards the end of Season 14 I don't like, again hard to put it into words.

Saying that, I do like the Jago/Litefoot relationship.

Season 12:

01=) The Ark In Space
01=) Genesis Of The Daleks
03) Robot
04) The Sontaran Experiment
05) Revenge Of The Cybermen

++ I like both of the stories in joint 1st place a lot and, depending on my feelings at the time, either of them could be ranked in first place whenever I was asked about them.


Season 13:

01) The Seeds of Doom
02) Pyramids Of Mars
03) The Brain Of Morbius
04) The Android Invasion
05) Planet Of Evil
06) Terror Of The Zygons


Season 14:

01) The Deadly Assassin
02) The Robots Of Death
03) The Masque Of Mandragora
04) The Hand Of Fear
05) The Talons of Weng Chiang
06) The Face Of Evil


Season 15:

01) Horror Of Fang Rock
02) Image Of The Fendahl
03) The Sunmakers
04) The Invisible Enemy
05) Underworld
06) The Invasion Of Time


Season 16:

01) The Androids Of Tara
02) The Stones Of Blood
03) The Ribos Operation
04) The Power Of Kroll
05) The Pirate Planet
06) The Armageddon Factor


Season 17:

01) Destiny Of The Daleks
02) City Of Death
03) Nightmare Of Eden
04) The Creature From The Pit
05) The Horns Of Nimon


Season 18:

01) The Keeper Of Traken
02) State Of Decay
03) Full Circle
04) Logopolis
05) Meglos
06) The Leisure Hive
07) Warriors Gate



Worst Episodes:

01) Warriors Gate
02) The Horns Of Nimon
03) The Leisure Hive
04) The Armageddon Factor
05) The Invasion Of Time
06) Underworld
07) Meglos
08) The Creature From The Pit
09) The Planet Planet
10) The Face Of Evil



Best Stories:

01) The Seeds Of Doom
02) The Deadly Assassin
03=) The Ark In Space
03=) Genesis of The Daleks
05) The Robots Of Death
06) The Keeper Of Traken
07) Pyramids Of Mars
08) Horror Of Fang Rock
09) The Androids of Tara
10) The Masque of Mandragora

Top 5:

1. State of Decay
2. The Talons of Weng-Chiang
3. Genesis of the Daleks
4. Pyramids of Mars
5. The Brain of Morbius

Bottom 5:

1. The Pirate Planet (worst)
2. Robot
3. Terror of the Zygons
4. Revenge of the Cybermen
5. Full Circle

Best:

Genesis of the Daleks
Pyramids of Mars
Robots of Death
Talons of Weng Chiang
City of Death


Worst:
Meglos
Underworld
Nightmare of Eden
Creature from the Pit
Leisure Hive (because it bores me..all flash)

I'll keep it simple.

Best: anything with Harry or Leela.
Worst: anything with Adric.

Despite being written by Douglas Adams? Dear oh dear.

At least Adams bounced back with "City Of Death" - and the incomplete "Shada".

Initially, Davison had to put with Adric, too!

Despite his pessimism, he did NOT deserve to die, at the end of "Earth-shock".

No, he deserved to die before the beginning of Full Circle.

Ha, I'm so mean.

What about Adric's deceased brother?

Varsh would have been preferable to Adric, I'll concede.

I don't like it, regardless of who it was written by (and I was well aware who wrote it, by the way).