- Operation: Afro Circus Rescue -- To save the four heroes from the Zoo.
- Roll of Euros --
- Match -- For the cannon numerous times.
- L.A.R.V.: Or Luxury Assault Recreational Vehicle. Kowalski has adapted an SUV into a vehicle that can be driven by the penguins.
- The Fisher Price toy of the L.A.R.V. shows it has forward-facing guns that pop out the sides and shoot plungers. These weren't in the movie, but the 'Assault' part of the acronym suggests that the L.A.R.V. may well be armed.
- Nuke-U-Lar Reactor: Gloria mispronounces it 'nuclear', and Skipper corrects her. It serves to give the L.A.R.V. a turbo boost.
- Saved the Madagascar Gang: When shot by DuBois when at the zoo, he managed to get to the circus and tell them what was going on.
- Mission Impossible -- The manner in which Alex, tied to a rope, attempts to infiltrate the casino is a parody of the similar, famous scene in MI.
- The Polar Express-- When Stefano asks Alex to follow him, they both run on the circus trains roof. Then the train reaches a tunnel and Alex jumps off into a train car.
- Lord of the Rings -- The recurring motif of a flaming ring representing the ring that Vitaly failed to jump through seems reminiscent of a similar motif in LOTR.
- Star Wars -- DuBois wields her snare like a light-saber against the onslaught of a chimpanzee-manned banana gun.
- The Matrix -- In the aforementioned banana gun scene, DuBois goes into bullet time, slices the first shot into two and dodges the second onslaught before striking back.
- Madagascar -- DuBois and her men were in crates (and this time headed for Madagascar) the same way Alex, Gloria, Marty and Melman were in the first film.
- Star Trek -- At the beginning, the penguins warp out.
- Jaws -- An excerpt of the main theme plays when DuBois is sniffing out the animals outside the Monte Carlo casino.
- Wipeout -- While announcing a challenge that is jungle themed, John Henson said that those who lose the challenge will be sent off the coast of Africa along with a giraffe, a zebra, a lion, and a hippo.
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