Amnesia

Amnesia was the (usually temporary) loss of memory.

On at least four instances, the Doctor suffered from partial amnesia after regenerating. (TV: Castrovalva, Time and the Rani, Doctor Who, The Time of the Doctor)

Instances of amnesia
The First Doctor and Susan Foreman suffered from partial amnesia when they arrived in 1963 London, apparently caused by challenging the Time Lord rule against interfering when they left Gallifrey. (PROSE: Time and Relative) According to another account, this memory loss occurred when the Doctor stole the TARDIS and it assaulted his mind. (PROSE: Echoes of Future Past)

The First Doctor, Ian Chesterton, Barbara Wright and Susan briefly suffered from amnesia after the TARDIS' fast return switch got stuck, which would have sent it back to the creation of a solar system and resulted in its destruction. The ship crashed itself in an attempt to warn its passengers of the dangers, and a small explosion occurred in the TARDIS as the Doctor tried to correct its faulty navigation circuits, rendering all four unconscious. (TV: The Edge of Destruction)

The First Doctor force-fed an amnesia pill to William Shakespeare to ensure that he would forget the advanced technology he had downloaded into his mind. (PROSE: The Empire of Glass)

The Masters of Dorada suppressed the memories of the Second Doctor, Ben Jackson and Polly, whom they enslaved when they arrived on Dorada. (PROSE: The Dream Masters)

The victims of the War Lords suffered from post-hypnotic amnesia due to the conditioning used to make them forget what had happened to them. (TV: The War Games)

During the Third Doctor's exile on Earth, the Time Lords suppressed his knowledge of how the TARDIS worked as part of his punishment (TV: The War Games), as well as some details of Earth's future history (PROSE: The Devil Goblins from Neptune). They restored this knowledge when they lifted his exile. (TV: The Three Doctors)

The victims of an alien Extractor suffered from permanent amnesia. Liz Shaw suffered from temporary amnesia following a car accident after escaping the Extractor. (PROSE: The Mind Extractors)

The Fourth Doctor suffered from amnesia after being transported to Deepcity due to a flaw in the Time ring. (PROSE: A Device of Death)

Alistair Gordon Lethbridge-Stewart suffered from amnesia from 1977 to 1983 as a result of meeting his future self, unable to recall the Doctor or the Doctor's companions, until the Fifth Doctor reminded him. (TV: Mawdryn Undead)

The Viyrans erased Peri Brown's memories of being patient zero of a mutagenic virus on Grallista Social to keep knowledge of the virus secret. (AUDIO: Mission of the Viyrans)

The Time Lord Azmael provoked selective amnesia to the Earthling twins Romulus and Remus Sylvest by applying a green circle on their wrists. (TV: The Twin Dilemma)

The Sixth Doctor suffered from partial amnesia after being transported to Space Station Zenobia for his trial. (TV: The Mysterious Planet)

Ace suffered from amnesia when the Seventh Doctor accidentally erased her memory while editing his own. (PROSE: Timewyrm: Genesys)

The Time Scaphe crew lost their memories after their ship collided with the TARDIS, but regained them after Ace told them the name of their home world, Gallifrey. The TARDIS took the Doctor's memories to keep them safe from the Process, but later returned them to save itself from destruction. (PROSE: Cat's Cradle: Time's Crucible)

The Seventh Doctor and the people who had consumed the essence of the Celestial Toymaker gave themselves electroshock therapy to suppress their memories of him in an attempt to destroy him. (PROSE: The Magic Mousetrap)

The Seventh Doctor briefly suffered from amnesia when he was thawed out after being frozen in ice for millions of years. (AUDIO: Frozen Time)

The Master suffered from amnesia while on Perfugium as the Doctor's deal with Death caused him to revert to the persona he would have been if Death had not marked him as her champion. (AUDIO: Master)

The Eighth Doctor suffered from amnesia after falling into the Master's trap, requiring him to be guided by Rassilon to regain his memories by visiting and mentally linking with his previous seven selves. (PROSE: The Eight Doctors)

The Eighth Doctor, Charley Pollard and Gideon Crane suffered from amnesia after the TARDIS crashlanded in Malebolgia, the TARDIS's damaged telepathic circuits dividing the Doctor's mind between Gideon and 'Zebediah Doe' and nearly erasing Charley's mind. (AUDIO: Minuet in Hell)

The Eighth Doctor suffered from amnesia after the brain-worm attacked him in the Cube. (AUDIO: Something Inside)

The Eighth Doctor suffered from amnesia after being forced to destroy Gallifrey (PROSE: The Ancestor Cell); this was initially attributed to trauma, but was later established as the Doctor erasing his own memory to create room for him to store the compressed Matrix in his subconscious (PROSE: The Gallifrey Chronicles).

The Eighth Doctor suffered from amnesia while on Espero, but his memories were just suppressed and quickly restored. (PROSE: Halflife)

Madeleine Fairweather suffered from amnesia from 15 January 1942 until shortly before her death on 1 January 2008. (AUDIO: The Girl Who Never Was)

The Ninth Doctor and Rose Tyler suffered from partial amnesia after being transported to Satellite Five. (TV: Bad Wolf)

The staff of Torchwood Three often employed a drug called retcon to induce amnesia about recent events and prevent the existence of aliens being made publc. (TV: Everything Changes)

Chris Cwej suffered from amnesia while on Ardethe. (PROSE: Deadfall)

The Panjistri supplied the Kirithons with zavát which, in addition to being their main food source, weakened their resistance to telepathic suggestion, allowing the Panjistri to suppress certain memories and even the Kirithons' awareness that they should have those memories in the first place. (PROSE: Timewyrm: Apocalypse)

Tricky Van Baalen lost his memory in a salvaging accident. (TV: Journey to the Centre of the TARDIS)

Emily Blandish suffered from amnesia after being hit on the head by a Dæmon. (PROSE: Child of Time)

Iris Wildthyme lost most of her memories when Panda smashed the crystal containing them. (AUDIO: Wildthyme at Large)