When Amy and Rory are running through the halls of the TARDIS it is only the second time, since the return of the show in 2005, that any part of the TARDIS other than the control room has been shown.
The junkyard, where "The Doctor's Wife" takes place, was written as a nod to The Doctor's first ever appearance An Unearthly Child (1963), where Ian and Barbara met the First Doctor and Susan at a junkyard in contemporary London and discover the TARDIS.
Neil Gaiman wanted to explore the dimensions of the TARDIS and hoped to feature the TARDIS swimming pool. It would have been deleted by the Doctor at the start of the story to help power the journey to the bubble universe, only to reappear later, providing the Doctor with evidence of House's manipulations. This was scrapped because Karen Gillan couldn't swim. He hoped to include it with Rory, but it was scrapped due to budget concerns.
While it has been hinted at before a few times in-universe, most directly in The End of Time: Part Two (2010), this episode offers the first concrete confirmation that Time Lords can change genders when they regenerate. This was a deliberate addition to the mythos on Neil Gaiman's part.
Neil Gaiman based House's personality and his treatment of Rory and Amy on AM in Harlan Ellison's famous short story "I Have No Mouth and I Must Scream". Gaiman posted on Tumblr that he hoped to make Harlan Ellison smile with the shout-out. Apparently, he did.