The Third Doctor once suggested to the Brigadier that the phrase was meaningless technobabble. (AUDIO: The Paradise of Death) With similar uncertainty, the Twelfth Doctor once "bet" that the phrase meant something and that it "sound[ed] great". (TV: The Girl Who Died)
The Third Doctor once reversed the polarity of the neutron flow to destroy a Sea Devil base. The Master understood the implications of his actions when the Doctor told him. (TV: The Sea Devils) The Third Doctor performed the action again whilst with his other incarnations in the Death Zone to free the TARDIS of a force field. (TV: The Five Doctors)
The Fifth Doctor reversed the polarity as part of a process to stabilise his post-regeneration. (TV: Castrovalva) He also reversed the polarity to aid in his and his companion's escape from Mawdryn's ship. (TV: Mawdryn Undead)
The Ganger clone of the Eleventh Doctor stated a mangled version of the phrase when reliving the memories of his predecessors. He went on to say that he had "reversed the jelly baby of the neutron flow", a trademark item of the Fourth Doctor. (TV: The Almost People)
The Twelfth Doctor once reversed the polarity of the neutron flow of a Mire helmet so Ashildr could wear it to create hallucinations of an unbeatable threat, forcing the Mire to retreat. (TV: The Girl Who Died)
While not neutrons, polarity was reversed by the Third, (TV: The Dæmons, The Time Monster, Frontier in Space, Planet of the Daleks, Invasion of the Dinosaurs) Fourth, (TV: City of Death) War, (TV: The Day of the Doctor) Tenth, (TV: The Lazarus Experiment, The Day of the Doctor) Eleventh, (TV: The Day of the Doctor, The Time of the Doctor) and Thirteenth Doctors, (TV: It Takes You Away) as well as Nyssa (TV: Arc of Infinity) and Clara Oswald. (TV: Hell Bent) Yasmin Khan was also familiar with the concept. (TV: It Takes You Away)
Behind the scenes
Although remembered as the Third Doctor's catchphrase, "Reverse the polarity of the neutron flow" was only uttered twice by him on television, and only one of these instances was during his own era. He much more commonly stated simply, "Reverse the polarity".