The English Way of Death
The Well-Mannered War
System Shock
An easier list to make. Tom Baker's time is quite patchy in terms of story quality. There are some absolute gems but then, for every gem, there's some rather dreadful stuff.
Genesis of the Daleks
Pyramids of Mars
The Deadly Assassin
State of Decay
City of Death
Robot (Giant Robot)
The Ark in Space
The Sontaran Experiment
Genesis of the Daleks
Revenge of the Cybermen
Terror of the Zygons (Loch Ness Monster)
Planet of Evil
Pyramids of Mars
The Android Invasion
The Brain of Morbius
The Seeds of Doom
The Masque of Mandragora
The Hand of Fear
The Deadly Assassin
The Face of Evil
The Robots of Death
The Talons of Weng-Chiang
Horror of Fang Rock
The Invisible Enemy
Image of the Fendahl
The Sun Makers
Underworld
The Invasion of Time
The Ribos Operation
The Pirate Planet
The Stones of Blood
The Androids of Tara
The Power of Kroll
The Armageddon Factor
Destiny of the Daleks
City of Death
The Creature from the Pit
Nightmare of Eden
The Horns of Nimon
Shada (Not Televised)
The Leisure Hive
Meglos
Full Circle
State of Decay
Warriors Gate
The Keeper of Traken
Logopolis