This episode marked the first time a new opening sequence was introduced to the show. It featured 3-dimensional renderings of the characters, a remix of the original theme tune and live-action 'action' clips spliced in between animated clips from previous episodes. This opening sequence remained with the show until the start of season 6.
"Ha ha, charade you are" comes from Pink Floyd's "Pigs (Three Different Ones)" on their 1977 album Animals. Cartman had used it before in Cat Orgy (1999).
When Timmy arrives back from time traveling, he has a bumper sticker on his wheelchair that reads: Enola Gay. The Enola Gay was a Boeing B-29 Super-fortress bomber. On 6 August 1945, during the final stages of World War II, it became the first aircraft to drop an atomic bomb.
There are various toys from Starvin' Marvin in Space (1999) in the nerds' basement, including a Marklar doll.
There is a running gag about a debate on the number of Star Trek (1966) episodes. There are only 80 episodes. The Cage (1966), which was the pilot, is numbered as episode zero.