Okay, time to explain some of the inside jokes:

1. The Doctor's introduction to Clark Savage was mostly lifted off a bit of dialogue from "Voyage of the Damned."
2. The mention of the werewolf was from "Tooth and Claw," another DW episode.
3. The mention of Bess, or Elizabeth the First, refers to a running joke from the current run of Doctor Who. It's implied that Bess and the Doctor had a scandalous relationship, one she never forgave him for. Of course, we'll find out more when November 23rd comes along.
4. Japanese Agent Moto is none other than Mr. I. A. Moto, created by John P. Marquand.
5. The basics of the detox scene came from the DW episode, "The Unicorn and the Wasp." In that case, the final shock was Donna kissing the Doctor.
6. Rose is banging a wall as an oblique reference to the mention of the drink, a "Harvey Wallbanger" from the episode mentioned in # 5.
7. The 10th Doctor enjoys bacon and baked beans. This is not true with the 11th Doctor, as evidenced by "The 11th Hour." Truthfully, it was a pretty bad first day.
8. As mentioned in a previous post, the Chief Constable is from "The Stolen Earth."
9. Salusian bluapples are from Ninja High School.
10. The mention of Donna being a household god is from the DW episode "The Fires of Pompeii."

And that should pretty much explain the jokes.

--Doc