The first time a werewolf appeared in the television series was in the Seventh Doctor serial The Greatest Show in the Galaxy (1988). A wolf-man appears in the 1986 Sixth Doctor story Mindwarp, and the primords in the 1970 Third Doctor story Inferno are also lupine in appearance, but in both cases these are induced mutations rather than people who switched between human and wolf forms.
Mags was a young woman who appeared human, the companion of the interplanetary explorer Captain Cook, who said that he found her on the planet Vulpana. The Doctor and Ace met the pair while investigating the Psychic Circus on the planet Segonax.
Ultimately, Mags was revealed to be a werewolf, her transformation triggered by moonlight. Cook triggered her metamorphosis in an attempt to kill the Doctor for the amusement of the primeval Gods of Ragnarok, but the Doctor convinced her that she could control her feral instincts, and Mags turned on the Captain instead. After the Doctor had defeated the Gods of Ragnarok, Mags elected to remain behind on the planet with Kingpin, the only survivor of the Psychic Circus.
No other details about Mags, her species, whether all of her race transform into werewolves, or even if she did originate on Vulpana itself were provided during the story.
A werewolf was the principal antagonist in the Tenth Doctor episode "Tooth and Claw" (2006). This werewolf was an alien entity that fell to Earth in Scotland in 1540, where it landed in St. Catherine's Glen near a monastery. The Doctor surmised that only a single cell survived, which was then incubated in various hosts via biting them, passing down through the centuries until it matured. The Doctor described it as a "lupine wavelength haemovariform". The werewolf showed an aversion to mistletoe, although whether this was a physical allergy or a conditioned reflex (as suggested by the Doctor) was not established.
The wolf cell was cultivated in young boys kidnapped by the monks of the monastery, the Brethren, who turned away from worshipping God and began to worship the wolf instead. The hosts would react to moonlight and transform into werewolves at the full moon, leading to dead livestock and legends of lycanthropy in the surrounding area.
Eventually, in 1879, the Brethren arranged for Queen Victoria to be diverted to the nearby Torchwood Estate where the current host would infect her with the wolf cell, leading to the creation of the "Empire of the Wolf". The plot was thwarted by the Doctor and Rose, who used a telescope constructed by the father of Sir Robert MacLeish against the werewolf. The telescope was in actuality a gigantic light amplification chamber and, using the Koh-i-Noor diamond as a focusing element, struck the werewolf with enough moonlight to dispel it from the planet. It is unclear, however, if Victoria was indeed infected in the end.
In the Eighth Doctor Adventures novel Kursaal by Peter Anghelides, the Eighth Doctor and Sam travelled to Saturnia Regina, which was about to be turned into a theme park planet and renamed Kursaal. However, beneath the proposed attractions were the homes of the Jax, a wolf-like species thought extinct. When the archeological teams investigating the Jax ruins were killed by a wolf-shaped creature, the Doctor and Sam investigated, discovering that the victims transformed into wolves when triggered by moonlight. The dead became mindless drones, while those infected but still living retained their senses, thereafter working to further the agenda of the Jax.
It was revealed that the Jax were not the wolves, but the virus that caused the transformation itself, controlled by ancient Jax technology contained within their cathedral. Sam was infected, but the Doctor managed to destroy the Jax technology and she was returned to normal with no ill effects.
In the Past Doctor Adventures novel Wolfsbane by Jacqueline Rayner, it was stated that in 1933, Nazi Germany became aware of the existence of werewolves and forced them to register with the government. A group of them were imprisoned in camp surrounded by silver barbed wire and pressed into state service. In 1934, these werewolves were used to commit the purge that became known as the Night of the Long Knives. One of these werewolves, Emmeline Neuberger, managed to escape into the German woods. The transformation of these werewolves are also tied to moonlight.
Neuberger surfaced in England two years later, unwillingly assisting Lady Hester Stanton who wanted to magically bind the land to herself. Harry Sullivan was present at the time, having been stranded there when the TARDIS inexplicably left without him- later implied to have been drawn off-course by its damaged future self-, Harry joining forces with the amnesic Eighth Doctor to thwart Hester's plans. The Fourth Doctor and Sarah returned for Harry, but not before Neuberger, desiring a mate, bit him. What happened to Harry next is unclear, due to various manipulations of time being done by the Council of Eight (Sometime Never...). While some of these manipulations were undone, it is unclear whether Harry's infection was one of them. However, given the character's subsequent history in other tie-in fiction, it can be assumed that his condition was eventually cured or at least controlled.
In the Decide Your Destiny novel, the reader was allowed to affect the actions with their choices. There were many choices, but all seemed to feature similar characters; The Eleventh Doctor, Amy Pond, Dr Lazenger (a werewolf keeping back his transformation by willpower) and Doctor Adams, one of Lazenger's employees. Werewolves descended from a Torchwood maid infected with the haemovariform were arriving in Aberdeen to have the original crashed haemovariform extract the werewolf part of them and transfer it to the world. The many endings include the plans goin ahead, the Moon being stopped, the Doctor deactivating it, the haemovariform being killed with mistletoe oil and Lazenger dying to stop it. In several different versions the character is turned into a werewolf and has to join the original werewolves to cure them.
In the Big Finish Productions audio play Loups-Garoux, the Fifth Doctor and Turlough encountered a race of werewolves in Rio de Janeiro in 2080. It was said that werewolves were one of the planet's oldest races and were extremely long-lived. One of them, Pieter Stubbe, even claimed to have been around at the time of the Earth's creation.
These werewolves were tied to the cycles and elemental power of the Earth, and were weakened if separated from it (even by being on the upper floors of a building). The werewolf mutation could be transmitted by a bite as well — Stubbe had transformed Illeana de Santos into a werewolf in 1812. By 2080, de Santos had become leader of the werewolves, and Stubbe attempted to reclaim her as his mate. With the aid of the Doctor and Turlough, Stubbe's hold on de Santos's pack was broken. Stubbe himself aged to death when he rushed into the TARDIS, enabling the Doctor to materialise the ship in orbit and severing Stubbe's connection with the Earth.
In the Doctor Who Weekly comic strip story Doctor Who and the Dogs of Doom (DWW #27-#34), the Fourth Doctor met a race of wolf-like humanoids called the Wereloks in the year 2430. While the Wereloks did not transform from human to werewolf, their fangs injected a venom that would transform those they bit into Wereloks when their bodies were subjected to light of a certain intensity, like moonlight. The Doctor was himself infected but managed to find a cure for his condition.
The Wereloks were used as a slave race by the Daleks, who sent them to raid the New Earth system (no relation to the planet seen in "New Earth") as a prelude to sterilising the system of human life so the Daleks could use it as a breeding ground. Together with the human colonists and the help of a tamed Werelok named Brill, the Doctor "time locked" the Dalek army and their Werelok soldiers in a single moment of time and space.
The various types of werewolf seen as described above share certain similarities: for example, the exposure to moonlight triggering the transformation and the transmission of the mutation by biting. The Jax infection also sounds similar to the one in "Tooth and Claw" (although the Jax had a technological base), and the Earth-bound wolves of Loups-Garoux bear some similarities to the ones featured in Wolfsbane.
Equally, it is tempting to draw a connection between the extraterrestrial werewolf of "Tooth and Claw" and Mags (and possibly Vulpana) in The Greatest Show in the Galaxy, but there is no explicit evidence that ties them, or any of these, together. It is equally possible that they are completely unrelated.