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In the Doctor Who episode "The Doctor's Wife" (season 6, episode 4), written by guest writer Neil Gaiman, the character 'House' places the TARDIS matrix in the body of a human woman, which allows the Doctor to communicate with… her.

Has there been any statement by the Doctor Who production team as to whether this episode is canonical? Are episodes by guest writers usually canonical, or not?

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    Well, according to Steven Moffat: "It is impossible for a show about a dimension-hopping time traveller to have a canon."
    – Chris Burt-Brown
    Commented Apr 24, 2012 at 14:22

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A lot of Doctor Who episodes are written by "guest writers", which basically just means that they're not regular DW writers. In any case, no matter who writes the episode, whether it's a normal DW writer or not, Steven Moffat, the current Doctor Who showrunner, signs off on the script to ensure continuity (well, as much continuity as one can get in a 48-year-old show) in both the current series and the Whoniverse as a whole.

So The Doctor's Wife was planned into the season by the normal production team; it's just that the script was proposed and written by someone who normally doesn't work in TV. That's fairly common, and doesn't make it different from other TV episodes, since Moffat is the one who oversees and approves the script (and in some cases, he'll rewrite it, although not in this particular case).

Now, the BBC has never issued an official comment on what is canon in the Whoniverse. Many people consider the TV shows and the 1996 movie to be the only canon sources; other people include the novels and other sources as part of canon.1

In any case, the vast majority of people (in fact, as far as I know, everyone) considers the TV show in its entirety to be part of canon. So yes, The Doctor's Wife is canon in the Whoniverse.

1 If you're curious, here are a list of possible canon sources. It's up to you to decide what you consider canon: The Old Series, the New Series, the 1996 movie, Torchwood, the Sarah Jane Adventures, K-9, the novels, the comics, the other two movies, the Magazine, the audio stories, the computer games, the webcasts, Doctor Who Confidential, Doctor Who and the Curse of Fatal Death (parody but written by Steven Moffat), the DVD extras, the charity scenes, etc...

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    Instead of saying it's not entirely unusual, I'd make the point that a script for a 1 hour TV show is 60 pages and it's a bit much expecting a producer to write 13 of those in a year (all though Straczynski did even more than that in Babylon 5). It is actually a standard practice to hire outside writers on most TV shows. And the showrunner not only signs off on it, but is intimately involved with the reviews and re-writing process of any script. So, as with any TV show, you can't toss out an episode as "doesn't count" because it's not by staff writers.
    – Tango
    Commented Apr 24, 2012 at 4:25
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    @TangoOversway Sure, I agree entirely. I guess what I was trying to say is to say that DW has some writers who are more regular than others that might be considered part of the DW team, such as Gareth Roberts, as opposed to Neil Gaiman, who's really a novelist, but that even one-story writers aren't unusual. I've edited to make that clearer, though.
    – waiwai933
    Commented Apr 24, 2012 at 4:30
  • I didn't want to edit your answer, since it was good - just wanted to back it up a little more. Also, I didn't want to get into how many BBC shows have a smaller number of writers than American shows. Freelance is much more common in America, where you're doing 22-26 episodes a year, where many BBC shows do 13 or fewer in a stretch.
    – Tango
    Commented Apr 24, 2012 at 4:54
  • And some of us desparately try to pretend the movie was not canon and just happened to star a guy that looked a whole lot like the real 8th doctor :\
    – KutuluMike
    Commented Jun 14, 2012 at 17:00

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