Pinky shouts at Brain "There's a human you?!". This is a callback to a similar line he says to Brain in Brainwashed Part 1: "There's a human version of you?".
Brain says that Tom Bodett is the "voice for those tedious Good Idea/Bad Idea segments." In addition, a certain "Emperor C. Boo" is on the guest list of the White House's press conference on the Brain. "C Boo" is a reference to the Animaniacs character Chicken Boo.
The ending with Brain & Pinky trying to escape the island and the prisoners chasing them and roaring the same noise as the pod people and then the shot where we find Brain is on their side and he points and roars like the final scene where we find Donald Sutherland is a podperson.