Fry and Bender have a conversation referencing the urban legend, widely circulated from the 1960s on, concerning baby crocodiles/alligators obtained by New Yorkers vacationing in Florida being flushed down the toilet when they proved to be too troublesome and/or large to make good pets, whereupon they grew to gigantic size in the New York sewer system. Further generations of alligators were said to have grown to become albinos, the darkness making pigmentation unnecessary.
There is a parody of the zealous worship of a nuclear bomb by underground denizens in "Beneath the Planet of the Apes". This was also parodied in Fallout 3 by the people of the settlement of Megaton, who worshipped an undetonated nuke which they named Atom.
While free-styling with his own head, Bender whistles Sweet Georgia Brown, the theme music of The Harlem Globetrotters.
In one scene, in the top left corner of the group of people in the sewer, you are able to see Turanga Morris and Turanga Munda, Leela's parents.
Fry and Leela enter the sewer world via the manhole cover from The PJs. The cover later appears in The Luck of the Fryrish. They later reciprocated by placing Fry's image on a milk carton.
As revealed later in the series, Nibbler and Nibblonians have been around since the Big Bang, making his age closer to 5 Billion than 5.