The Doctor's Wife

The Doctor's Wife was originally described as the ultimate TARDIS runaround episode, but of course it turned out to be much more than that.

The TARDIS Runaround

The TARDIS interior is discussed more in the post about Journey to the Center of the TARDIS. However, it's worth pointing out that this episode follows the Logopolis/Castrovalva tradition just as much as that one follows the Invasion of Time tradition: Most of the TARDIS is made up of rooms and corridors that look similar to the console room. Logopolis also introduced the Architectural Configuration System, which (among other things) allowed the Doctor or the TARDIS herself to adjust the configuration of rooms, create new rooms, or jettison rooms (which could be used for "ballast" or "thrust"), which shows up here again.

In this episode, we learn that the Architectural Configuration System contains console rooms that have been jettisoned, and even rooms that haven't been created yet—which is cool, but not a shocking addition to the TARDIS mythology. We also learn that time can behave oddly inside the TARDIS, something the NAs and EDAs both covered but which hasn't yet been seen on TV.

Idris

The real point of the story, of course, is Idris, a woman who gets the TARDIS matrix dumped into her head.

The idea of a humanoid TARDIS is not new, it permeates the EDA novels—although Gaiman may not have known that.

Alien Bodies introduces Marie, a humanoid TARDIS from the future (in a timeline that ended up never happening), who became stuck in the form of a women's police constable after visiting London in 1963. We learn that in the future, as part of their War effort, the Time Lords began breeding TARDISes that can take humanoid (well, Gallifreyanoid) form because it makes them more effective. Besides being able to walk around and talk to people, they can directly see how the abstract block transfer computations they run on interact with the world their pilots have to live in. We get a bit more of that in other novels, like The Taking of Planet Five.

But it's in Interference where things start to get interesting. The Doctor picks up a new companion named Compassion, who's a member of the Remote. The Remote are a colony of humans created by Faction Paradox, who connect directly to their media signals at a subconscious level. They're also are effectively immortal, but in a very odd way—when one dies, a new body is grown in the Remembrance Tanks, based on the memories of all of the living people who interacted with her—so eventually, everyone becomes their own public personas. The Compassion the Doctor meets is on her sixth life.

Over the next few novels, Compassion becomes increasing dysfunctional, being separated from her culture's media signals, and she begins picking up stray signals from the TARDIS instead. The Doctor tries to encourage her to interact more with human society (and with her fellow companion Fitz, although he has his own remote-and-TARDIS-related issues), but she withdraws further. A complicated sequence of events over multiple novels culminates in Shadows of Avalon: the Doctor's TARDIS is destroyed, but Compassion becomes a TARDIS.

This is a unique event, with almost no hope of anyone ever recreating it; the Time Lords realize that the only way they're going to get the humanoid TARDISes they need for the War (and know they will have during the War) is to kidnap Compassion and force her to breed.

Meanwhile, over the subsequent novels, the Doctor is able to interact with Compassion both as a TARDIS (e.g., the way she controls her interior) and as a humanoid. He learns, for example, that the randomizers that he's installed into his TARDIS in the past to avoid detection by the Time Lords are not only painful, but feel like a violation, in an almost rapey way. He's forced to reconsider the entire pilot-TARDIS relationship.

The story has two different endings. In The Ancestor Cell, we learn that the Doctor's TARDIS hasn't really been destroyed, but has become linked to Gallifrey and the War in a complicated way, which is only resolved when the Doctor destroys Gallifrey. Compassion sets his TARDIS to regrow (although will take over a century to complete), and leaves him for a TARDIS mechanic, someone who loves her like a man loves a car rather than with the Doctor's complex relationship to his TARDIS. Later in the EDAs, the Doctor runs into Compassion, who's apparently checking in on him to see if he's ready for the next stage of her plan, but we never get to see how that turns out. Meanwhile, the Faction Paradox spinoff series is set in a timeline where Ancestor never happened, the War wasn't averted, and Compassion becomes a major player in a game that may be even greater than the War, until she ultimately turns herself into the City of the Saved, which is another huge story not relevant here (but definitely worth reading).

Obviously this isn't at all the same story. In fact, in many ways, it's the exact opposite. Compassion is a human who has to come to terms with being a TARDIS; Idris is a TARDIS who has to come to terms with being a human. Compassion is a new TARDIS, something the Doctor hasn't dealt with in centuries; Idris is the Doctor's own TARDIS. The Doctor's love for his TARDIS is played off as a bittersweet and touching relationship in Idris's eyes (although it's also played for laughs in Amy's), but it looks deeply disturbing from Compassion's. Most importantly, the Doctor and his TARDIS have always been equal companions, while Compassion was a companion who often found herself as a spectator in events beyond her control, comprehension, or interest, until suddenly she became the most important thing in the universe and saw the Doctor as little more than a pawn.

Also, because the EDAs had the Doctor and Compassion interacting for a half dozen novels instead of one 45-minute episode, there was ample room both for more depth, and for long stretches where the core themes were basically ignored and Compassion was just another companion or just a TARDIS.

Still, both stories serve to let us—and the Doctor—look at the pilot-TARDIS relationship from a new angle, primarily because he can finally talk to the TARDIS. While Journey to the Center of the TARDIS lets us see the TARDIS as a machine, and as a world, The Doctor's Wife lets us see the TARDIS as a character.

Also, in both the post-Ancestor Cell novels and the post-Doctor's Wife episodes, the TARDIS often seems a little dark and threatening; after being forced to see just how big, how powerful, and most of all, how alien a TARDIS is, even when in human form, it's hard to take it for granted as just a magical box for adventures. Ancestor and The Name of the Doctor both had a dying TARDIS looming over the proceedings; The Gallifrey Chronicles and Journey had a damaged and dangerous and largely unknown TARDIS for part of the setting. Multiple stories in both ranges show the TARDIS accomplishing things that we'd never seen before, with no real explanation, reinforcing the idea that the TARDIS is far beyond our comprehension, and the little time we had getting to know her wasn't nearly enough. These stories wouldn't have worked nearly as well without Shadows of Avalon and The Doctor's Wife. You can see that in the NAs, which tried similar stories following Time's Crucible, but to less substantial effect. For that matter, the hints of people lost in the TARDIS that the Doctor has forgotten, but the TARDIS probably hasn't, seem less comical in the later stories of each range than they had in, e.g., Interference or the spinoff Adventure Games.

Again, Gaiman probably didn't know most of the history—he read the Target novelizations of the classic series voraciously, but, unlike Moffat, he'd never read any of the original novels. And it doesn't seem like Moffat made any major changes to his story. So, it's just a coincidence that he opened up so many of the same themes that Larry Miles and Paul Cornell had in the novels. But it may not be a coincidence that Moffat chose to follow up on them.