The bitten-off Bridge and Leela soaring through space is like Data going from the stricken Enterprise to the Reman warbird Scimitar in the Star Trek movie Nemesis.
Captain Lando Tucker connected to the wall of the Whale's bowels is a play on Pirates of the Caribbean where in the brig, Bootstrap Bill Turner is connected to the wall of the ship.
The Planet Express Crews roles parallel to the crew in Moby Dick. Dr. Zoidberg parallels the protagonist, Ishmael since they are both social outcasts and survived. Leela parallels to Captain Ahab because like Ahab, Leela became obsessed with killing a whale but the difference between them is that Ahab lost a leg while Leela only lost the monument.
When people come outside the whale, the scene is reminiscent of the end of "Close Encounters of the Third Kind".
The Fourth Doctor exits the whale, along with the rest of the whale's victims, a reference to the BBC's Doctor Who, who also travels through time, space, and dimensions.
When Amy asked to cut the rope, Leela said "Negative Sailor Moon." This would be the first out of 2 references to that, the other being the Japanese version of Amy in "Reincarnation".
When mourning the loss of their daughter, Inez says "My days of joy and luck are over! Guess I gotta quit that club." This is a reference to The Joy Luck Club written by Amy Tan .
Before losing the monument, Leela was piloting through a starship grave yard. One of the ships was an Oceanic Airplane, possibly parodying J.J. Abrams hit television show Lost.