Pear

Pears were a type of fruit. There were various varieties, some of which could easily be mistaken for apples. (PROSE: Slow Decay)

Pears were served at King Gilgamesh's court in Uruk in 2700 BC. (PROSE: Timewyrm: Genesys)

A bowl containing pears was present at Sutcliffe Manor during the 1814 frost fair. (TV: Thin Ice)

When the Seventh Doctor turned himself into John Smith, he left instructions for Bernice Summerfield, one of which was to not let him eat pears, as he did not like them and did not want to wake up tasting that. (PROSE: Human Nature)

The Tenth Doctor hated the taste of pears, (PROSE: The Taking of Chelsea 426) at least in ice cream. (AUDIO: One Mile Down) After he turned himself into John Smith in November 1913, he ate a pear as he wandered near his biodata module. (TV: Human Nature) When the Tenth Doctor was restored, he was disgusted by the taste left in his mouth. (PROSE: Twice Upon a Time)

The Twelfth Doctor also warned Clara not to eat pears as they were too "squishy" and always made your chin wet, just before he lost his memories of her. He stated that it was extremely important, and told her to write it down. (TV: Hell Bent) The Twelfth Doctor later gave his future self some advice before regenerating, one of which was "never, ever, eat pears" (TV: Twice Upon a Time) He considered his disdain for pears "his personal taste" and "a quirk born of experience" which he didn't want squandered by any of his future incarnations. (PROSE: Twice Upon a Time)

Pears were Rory Williams' favourite fruit. (PROSE: Borrowed Time)

By the 67th century, Gifftan culture confused fruits such as pears and avocados for a legendary Earth hero called Avocado Pear. Such meant that Yoss Inkl named his son Avocado in honour of the humans Ryan Sinclair and Graham O'Brien who assisted him during his birth. (TV: The Tsuranga Conundrum)

Behind the scenes
A deleted scene of Human Nature, referencing the original novel, has the Tenth Doctor instrucinng Martha Jones not to let him eat pears when he turns into John Smith, as he would not want to have the taste in his mouth when reverted back into a Time Lord. Referencing this, the Doctor’s phobia was was mentioned again, media starting with The Taking of Chelsea 426. The running gag made its way to the TV series in Twice Upon a Time. The novelisation, like both versions of Human Nature, was by Paul Cornell.