When Frydo's (Fry's) two alter egos are fighting with each other, he asks, "S'awright?" and the other replies, "S'awright!", a routine made famous by the Spanish ventriloquist Señor Wences, and his character Pedro, a disembodied head in a box.
The title of the movie is a play on words of the novel titled "Ender's Game", a well-known and admired Sci-Fi work by Orson Scott Card.
When we first see the Dark Matter mine, a truck comes out. The alien-language phrase written on the side of the truck reads "OBEY MOM".
During the opening credits, the (only) yellow alien language sign reads "TASTY HUMAN BURGERS".
The string of digits during the opening Yellow Submarine (1968) parody is part of the decimal expansion of Euler's constant "e".