The Planet Express ship is powered by Whale Oil. In Futurama continuity, all spaceships had been powered by dark matter, until the crew rendered all dark matter in the universe inert in Futurama - El juego de Bender (2008), after learning that dark matter was extracted in a cruel manner from Nibbler's species, Nibblonians.
One of the Justices of the Supreme Court is a woman listed as "Sagal". Her hair and name suggest that she is Katey Sagal, the voice of Leela.
The Alienese in the opening sequence reads: "The humans shall not defeat us."
The Frank Sinatra-esque opening song is performed by Padre de familia (1999) creator Seth MacFarlane.
According to David X. Cohen on the commentary track (DVD), the coordinates of the Violet Dwarf have special significance. Part of the coordinates refers to "Mark 948" and when rephrased as Mark 9:48, the corresponding Bible verse (International Standard Version) is: "In that place, worms never die, and the fire is never put out." This is clearly an allusion to the climax of the movie.