Nudity

Nudity, referred to as being naked, was the state of wearing no clothing. According to the Eleventh Doctor, everybody was "naked underneath", an observation which disturbed Clara Oswald. (TV: The Time of the Doctor) To wear minimal clothing was to be half-naked. (TV: The Unquiet Dead)
Rhys Williams referred to his being in the nude, on waking up, as his "morning glory". (TV: Out of Time)
In 1869, Gwyneth, having seen into Rose Tyler's mind, saw that people in her time were half-naked. (TV: The Unquiet Dead)
Raxacoricofallapatorians, such as those from the Slitheen family, did not wear clothes naturally, but did use compression field collars to fit into skin suits for infiltration purposes. (TV: Aliens of London et al.) "Poisoned by the gas exchange" while wearing a suit made from the human Joseph Green, Jocrassa Fel-Fotch Passameer-Day Slitheen was encouraged to shed his suit by his fellow Slitheen. Finally, Jocrassa proclaimed that "victory should be naked." (TV: World War Three)
Historians who had been allowed access to the "Monster Vaults" of the databanks in the Doctor's TARDIS observed that the Abzorbaloffs of Clom, as a result of drawing sustenance through their skin, needed to be as naked as possible and so naturally wore little more than a thong. They noted this predilection was shared with the Slitheen from Clom's twin world of Raxacoricofallapatorians. (PROSE: The Monster Vault)
After being returned to his proper adult form from being a baby, a confused Sergeant Benton was seen naked and bewilderingly asked everyone present to explain the events that had just transpired he had supposedly missed that led to him being naked. (TV: The Time Monster)
The shapeshifting Zygons appeared without clothing in their true forms. (TV: Terror of the Zygons)
The defabricator could instantly deprive the human body of clothing. Jack Harkness was subjected to such a device while starring on What Not to Wear on the Game Station. He was, however, able to preserve a compact laser deluxe by hiding it somewhere "you really don't wanna know", proceeding to restore his clothing after destroying droids Trine-E and Zu-Zana. (TV: Bad Wolf)
When Martha Jones was captured and copied by the Sontarans during their 2009 invasion of Earth, her clone emerged from the cloning pool naked. Martha was later stripped of her clothes, which were taken by her clone to maintain the disguise, and left in a deep trance, wearing only a white medical gown for modesty. After rescuing her, the Tenth Doctor gave her his coat so she could cover herself. (TV: The Sontaran Stratagem, The Poison Sky)
Having been "born" from the Tenth Doctor's hand, the Meta-Crisis Tenth Doctor emerged inside the Doctor's TARDIS naked, as Donna Noble awkwardly pointed out. The Doctor promptly acquired clothing to wear after making the TARDIS dematerialise from the Crucible. (TV: Journey's End)
Visitors to Tasha Lem's Papal Mainframe were required to be naked. The Eleventh Doctor obliged to this as he visited the Papal Mainframe just prior to the Siege of Trenzalore. For the benefit of his human companion Clara Oswald, the Doctor projected hologram clothes onto her visual cortex, which made her perceive the naked Doctor as still being dressed. When the two were invited aboard the Mainframe, he had Clara swallow a hologram projector which created a hologram shell that fashioned a holographic outfit to cover her own nudity. (TV: The Time of the Doctor)
The Twelfth Doctor remarked that Rusty, having removed his gunstick as proof to show he agreed to the Doctor's terms while talking to him, was "the very first Dalek that ever got naked for [him]." (TV: Twice Upon a Time)
Naked hide and seek was a game one could play while naked. (TV: Adrift)
The Tenth Doctor claimed he once swam the English Channel naked. (COMIC: The Betrothal of Sontar)
== Behind the scenes ==
The scene in TV: Bad Wolf where Jack Harkness is disrobed was originally filmed full-length, with rear nudity. According to John Barrowman, this shot was vetoed by the BBC. (CON: The World of Who)
HOMEVID: Zygon: When Being You Just Isn't Enough notably featured full-frontal nudity, as well as sexual acts.