a real world point of view
The Doctor Who universe, or Whoniverse, is a term used by fans and, increasingly, the mainstream press. Much like the related term of canon its scope is somewhat debated by fans.
Generally speaking the Doctor Who universe is the shared fictional universe in which Doctor Who and spin-offs from Doctor Who take place. Fans disagree on whether some stories and spin-offs are considered part of the Doctor Who universe, and some dispute the concept's meaning or utility alogether. However, the concept potentially includes all the TV broadcast based spin-offs, video-only release spin-offs, prose and comic based spin-offs.
This wiki has established rules about what is and is not part of the Doctor Who universe for its own purposes (see our canon policy for more information), but this wiki has no authority beyond its borders. Much like canon, consumers of Doctor Who-related media are free to decide for themselves what stories are part of the Doctor Who universe, or indeed whether the concept exists at all in a meaningful fashion.
The BBC has never made a definitive pronouncement on the concept of "canon" for Doctor Who. This is notable because in order to build a "fictional universe" you need to have an established list of stories that act as the building blocks for that universe.
Doctor Who has had hundreds, likely thousands of contributors to its mythos — its universe, with each new story being a new contribution to the universe; the world of Doctor Who.
The actual phrase "Doctor Who universe" and "Whoniverse" are terms that are used frequently throughout in BBC publications. In many BBC publication they have phrased the continual development of the Doctor Who universe in therms of 'continuing adventures' rather than a prescribed universe. 
However, when creating their episode guide on their website the BBC republished several analysis from The Television Companion, several of which mentioned the concept of a "Doctor Who universe". In discussing The Ribos Operation it is stated that the establishment of the Black and White Guardians form important new characters within the "Doctor Who universe" . While in the episode guide for The Celestial Toymaker "The Celestial Toymaker's greatest legacy to the Doctor Who universe." It is this term and the idea of 'legacy' and 'mythos' where much of the idea of a "Doctor Who universe" continues development. As event at its earliest development Doctor Who was never limited to TV and never had a prescribed canon, it is a broad universe of adventures.
The term "Whoniverse" dates at least as far back as Peter Haining's 1983 reference book, Doctor Who: A Celebration. At that time, the Whoniverse had a very broad meaning, which included not just the setting of Doctor Who stories, but everything about the series, including behind-the-scenes information and fandom itself.
"Whoniverse" gradually became a more specific term. Initially it served to indicate that Doctor Who stories told in other media were part of the same universe as those told on television. This came to have greater importance in the media and to new fans who were approaching Doctor Who through TV-based series such as Torchwood, The Sarah Jane Adventures and K9.
The Doctor Who universe is the shared universe created and collected from the stories that are told about it.
With the return of Doctor Who on television in 2005 it began to include references to past stories, tying together various series of various media together into a single universe. Series 1 of Doctor Who included references to the planet Lucifer, kronkburgers and Justicia, and Series 5 revealed that Winston Churchill had met the Doctor before Victory of the Daleks, while the Slitheen-Blathereen family, descendants of the Blathereen, appeared in Series 3 of The Sarah Jane Adventures, all hinting that non-televised Doctor Who stories might take place in the "official" Doctor Who universe.
Martha Jones's employment by UNIT was first mentioned in the Torchwood episode Reset, in which she appeared and The Sontaran Stratagem/The Poison Sky had a semi-sequel in the form of the The Sarah Jane Adventures story The Last Sontaran. The Stolen Earth/Journey's End brought together cast members of three series. A number of more casual mentions have also taken place, such as Sarah Jane suggesting "Harry" and "Alistair" as possible names for Luke in Invasion of the Bane. Likewise, Sarah's description of the origins of her coulrophobia in TV: The Day of the Clown returns the viewer to the setting of A Girl's Best Friend. While such "crossovers" can be narratively insignificant, they nevertheless reinforce the notion of a single, shared universe.
Other fictional universes Edit
- See Canon#Other universes for detailed information.
There have been various deliberate attempts to create separate "fictional universes" that have elements of the Doctor Who universe, but are entirely separate entities. This is in a in-universe fictional sense, in a narrative sense and in a commercial sense.
These other fictional universes are not alternate timelines or parallel universes. These two concepts exist within the Doctor Who universe as defined and contained concepts within the scope of that fictional universe, whilst these other fictional universes are separate, merely using familiar concepts and entities as the Doctor Who universe.
The first example of this is the two films of the 1960s Peter Cushing; Dr. Who and the Daleks and Daleks' Invasion Earth 2150 A.D. Both these films and any prose (and others) stories connected to them establish an entirely different separate fictional universe in which their events take place. Different fictional universe rules apply to the characters and events that take place within the fictional universe.
Other examples of other fictional universes are works that are, from their outset, or sometimes retroactively stated to not be set in the Doctor Who universe through proclamation by the creators or publishers. Both Scream of the Shalka and Death Comes to Time were retroactively declared by their creators (and in the case of Shalka by the BBC) as not part of the Doctor Who universe.
Big Finish Productions' Doctor Who Unbound series from its outset was created to explore other fictional universes, where the elements of the Doctor Who universe existed but were not constrained by the Doctor Who universe.