On the map in Nixon's underground bunker, the planet Uranus is labeled "Urectum," in accordance with a joke made in the season one episode "A Big Piece of Garbage" (1999).
Hermes refers to the Janeway's Guide. This is a reference to Captain Kathryn Janeway, from Star Trek: Voyager (1995).
At the launch site, aptly named Cape Knievel (spoofing both NASA's Cape Canaveral and legendary daredevil/stunt performer Evel Knievel), a passing aircraft resembling a notoriously unsuccessful early prototype for manned flight can be seen clumsily flying past. It carries the name "Sanguinette," which by the definition of "sanguine," means it likely runs on blood.
The episode title, "In-A-Gadda-Da-Leela," is a double reference, both to the character Leela and Iron Butterfly's song "In-A-Gadda-Da-Vida," whose title is a garbled transcription of the original lyrics "In the Garden of Eden," which is a theme of this episode.
According to the DVD commentary, the plot of the episode stems from a famous science fiction story in which two astronauts crash land on an Eden-like planet and decide to repopulate their race. At the end of the story, the astronauts are introduced as Adam and Eve.