Bob Denver who played Gilligan on Gilligan's Island made an appearance at the white house gathering. Like Brain, he too refused to do the Smerschahoven (but for different reasons), so he to was imprisoned in the "Land Of Hats".
Brain: I have shrunken us to molecular size. We are traveling through an artery inside the human body. That thumping is the beating of the heart pumping which is propelling us to our destination: the larynx of folksy radio personality Tom Bodett. There I will implant my trachiomatic control chip. When middle America hears my plea for submission uttered in Tom's dulcet tones, they will be unable to resist. Allowing me to take over the world!
Hillary Clinton: Would you mind telling me who you are?!
Brain: As if you didn't know.
Hillary Clinton: Right. As if I didn't.
Pinky: Why, he's your guest of honor - the Brain!
Brain: I am the subject of this whole conference.
Hillary Clinton: We're here to discuss the human brain.
Pinky: Egad! There's a human version of you? Spooky!
Machine: (when trying to erase Pinky's memories) Error: subject has no mind to erase.
This cartoon was first aired as part of episode 62. The gag credit for this episode is: Flexanimous - able to change others minds.
The opening scene of Pinky and The Brain shrunk to microscopic size, piloting a ship in someone's body, and being attacked by white blood cells is an homage to classic sci-fi film The Fantastic Voyage.
The title of this part is a play on the old children's rhyme "Rain, Rain, Go Away."
The song Schmeerskahoven and the dance that goes with it are a parody of The Macarena, a Brazilian song and dance that became a sensation in the mid-1990's.
The entire hat town subplot is an homage to the Prisoner, the British show from 1967 created by and starring Patrick McGoohan as number 6. Number 6 is a spy who decides to leave the world of intrigue and after resigning wakes to find himself in the Village, where everyone is referred to by a number. Strawboater physically resembles and is dressed as Patrick McGoohan as number 6. Additionally, Number 6 frequently said "I am not a number!" This lends itself to Brain's "I am not a hat!" which is also the subtitle of part 2.
The "Schmeerskahoven" is performed by the unsuspecting band BAAB. This is clearly a parody of ABBA.