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)

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)

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)

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 at the Siege of Trenzalore. For the benefit of his human companion Clara Oswald, the Doctor provided her with a swallowable hologram projector which created a hologram shell for her to wear while projecting hologram clothes onto her visual cortex, which made her perceive the naked Doctor as still being dressed. (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)

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.