Pronoun

After the Twelfth Doctor regenerated into the Thirteenth, the Encyclopedia Gallifreya pondered as to how to approach the use of pronouns in the Doctor's records, wondering whether or not they should go through every entry about the Doctor and change each "he" to "she". The sentient encyclopaedia ultimately opted for singular they. (PROSE: Citation Needed) According to the Seventh Doctor, pronouns were always a trouble for Time Lords due to their ability to regenerate. (AUDIO: Dark Universe)

Shortly after said regeneration, as she fell through the sky above Sheffield from her TARDIS, the Thirteenth Doctor internally conversed with herself. After she erroneously referred to herself as "he", she reminded herself to be careful, as her "personal pronouns are drifting". (PROSE: Things She Thought While Falling)

Alex made sure to get the right personal pronoun as he translated the Sycorax leader's message "surrender or they will die." As it turned out, "they" referred to the population of humans with A-positive blood. (TV: The Christmas Invasion)

When talking about the Meep the Fourteenth Doctor promised to get "him" home, prompting Rose Noble to question why the Doctor assumed The Meep's pronoun. The Doctor agreed this was a good point and rectified this by asking the Meep if the Meep used "he, or she, or they". In response the Meep stated the Meep's chosen pronoun was the definite article. (TV: The Star Beast)

The Doctor
As far as this site is concerned, the Doctor's pronouns depend upon the context. Each incarnation of the Doctor is referred to with their respective pronouns (, almost always either he/him or she/her), whilst they/them pronouns are used in reference to the Doctor, taken more broadly, irrespective of incarnation. This use of singular they to refer to the Doctor beyond individual incarnations has, since 2017, moved beyond the editorial, and has been reflected in numerous stories, most often used by characters who know the Doctor well, like River Song, several incarnations of the Master, and Jack Harkness.

This rule also applies to other Time Lord characters who have changed gender, such as the Master and the General.

Daleks
Daleks have been alternately referred to with he/him pronouns, or as "it". Those referred to by masculine pronouns include numerous Supreme Daleks, (TV: Planet of the Daleks, The Witch's Familiar) the Dalek Emperor, (TV: The Parting of the Ways) Dalek Sec following his combination with Diagoras, (TV: Evolution of the Daleks) Dalek Caan (TV: The Stolen Earth) and Dalek X. (PROSE: Prisoner of the Daleks)

Otherwise, the majority of basic Daleks are referred to as "it", including the Metaltron (TV: Dalek) and Rusty. (TV: Into the Dalek)

Cybermen
In TV: Attack of the Cybermen, the Cyber-Controller is referred to with he/him pronouns.