- Paperclip -- To pick the lock on the penguins container.
- Cherry -- To help disguise Private and fight the Foosa.
- Gilligan's Island: -- A group of castaways are washed up ashore on a island in the ocean from a boat and can never leave the island without failing at every attempt to get off
- Stalag 17 (1953) -- Escapees in both films are called Manfredi and Johnson.
- The Flintstones (1960) -- When Alex divides the island Marty doesn't care and trots away singing parts of the theme to the Flintstones.
- Lord of the Flies (1963) -- Dead pilots in parachutes; blowing on conch shells.
- National Geographic Specials (1964)
- Born Free (1966)
- Star Trek (1966) -- Skipper says "Captain's Log."
- Planet of the Apes (1968) -- Alex yelling on the beach when the rescue fire burns up.
- Hawaii Five-O (1968) -- As Marty the Zebra comes to the island, he's surfing in to the theme from "Hawaii Five-O."
- Willy Wonka & the Chocolate Factory (1971) -- Alex hears "The Candy Man."
- Chariots of Fire (1981) -- Running on the beach with "Chariots of Fire" playing.
- Today (1982) -- Mentions Matt, Katie, and Al.
- Good Morning, Vietnam (1987) -- Juxtaposes song "It's a Wonderful World" with scenes of violence.
- Live with Regis and Kathie Lee (1988)
- Batman (1989) -- When Skipper the Penguin quotes Jack Nicholson as the Jack Napier when he says "we've been ratted out, boys."
- The Madness of King George (1994) -- Charlotte's quote "Smile and wave..."
- Ravenous (1999) -- The way that Alex licks Marty when he's sleep is like Colqhoun in Ravenous licking the soldier.
- American Beauty (1999) -- Alex is laying on the beach with steaks coming from above.
- Shrek (2001) -- Characters Shrek and Fiona named by Alex while being delirious searching the others in the beach.
- Moulin Rouge! (2001) -- Gloria turns into a green fairy.
- Napoleon Dynamite (2004) -- In the end credits, Melman dances the Napoleon.
- Gettin' It (2006) -- Poster outside of movie theater.
- Grave Decisions (2006) -- Movie poster when Sebastian walks down the street in the city wanting to buy a guitar.
- Flushed Away (2006) -- Alex the lion doll in Roddy's owner's room.
- Who Wants to Be a Millionaire: Episode #7.49 (2008) -- Included in a $2,000 question.
- QI: Film (#6.11) (2009) -- Listed as containing a Wilhelm Scream.
- Monsters vs Aliens (2009) -- In the scene where Gallxhar in "Monsters vs Aliens (2009)" is spreading his message around the world, a clip from "Madagascar (2005)" can be seen playing in the background on a screen in Times Square.
- Jeopardy!: Episode #26.26 (2009) -- Reference in a $1,200 clue in the category "Stars by Movie Roles."
- Monsters vs Aliens: Mutant Pumpkins from Outer Space (2009) (TV) -- Old woman resembling Nana from train station in "Madagascar" answers her door for B.O.B.
- The Penguins of Madagascar: Zoo Tube/Snakehead! (#1.27) (2010) -- A cab driver discusses seeing a video of an old lady hitting a lion.
- Who Wants to Be a Millionaire: Episode #8.144 (2010) -- Subject of a $3,000 question.
- Jeopardy!: 2010 Kids Week Game 1 (#26.211) (2010) -- Correct response in "Animated Films" category.
- Kirby's Dream Adventure (#487) (2011) -- When Karby and Kexas were captured by an invert, Kexas yelled "GET ME OUT OF HERE RIGHT NOW!". This is similar to Melman yelling "GET ME OUT OF THIS THING RIGHT NOW!" when he was stuck in his crate.
- HBO First Look: Madagascar: Welcome to the Jungle (#12.11) (2005) -- Many clips shown.
- Troldspejlet: Episode #34.2 (2005) -- Reviewed + footage used.
- Troldspejlet: Episode #35.4 (2006) -- DVD release reviewed + footage used.
- Madagascar 2 (2008) -- Scenes from the first movie are shown in the news report.
- Monsters vs Aliens (2009) -- In the scene where Gallaxhar is spreading his message around the world, a clip from Madagascar can be seen playing in the background on a screen in Times Square.
- Medium: Bring Me the Head of Oswaldo Castillo (#5.18) (2009) -- Maria watches the movie on TV.
- Fantasia (1940) -- Alex conducts the masses at the zoo in an identical way to Mickey Mouse in the Sorcerer's Apprentice scene in Fantasia.
- The Twilight Zone: To Serve Man (#3.24) (1962) -- One of the lemurs holds up a book entitled "To Serve Lemur" and says "It's a cookbook."
- Mutual of Omaha's Wild Kingdom (1963) -- Plays the theme song and recreates the lion pouncing on prey scene from opening credits.
- Planet of the Apes (1968) -- After Melman accidentally burns down the wooden Statue of Liberty we see Alex the Lion kneeling in front of it paraphrasing the famous Charlton Heston scene from the end of Planet of the Apes. Alex says "You maniacs, you burned it up. Darn you! Darn you all to heck!"
- The New Price Is Right (1972) -- The "do not spay or neuter your pets" quip.
- Saturday Night Fever (1977) -- Marty is strutting down a NYC street to the Bee Gee's "Stayin' Alive."
- The Mission (1986) -- Alex, the lion gets a cactus stuck to his back. The cactus is shaped like a cross. He then falls into the river and flows down a waterfall just like the movie "The Mission (1986)."
- The Silence of the Lambs (1991) -- The penguins joke to the other animals that they will kill them and eat their livers, as did Hannibal in Silence of the Lambs.
- Little Ghost (1997) -- "Smile and wave" is used in both.
- American Beauty (1999) -- Plays the American Beauty & spoofs the rose petal scene when everything Alex sees becomes a steak.
- Cast Away (2000) -- Volleyball named "Spaulding" with hand-print face.
- Zoolander (2001) -- Alex posing at the zoo does Zoolander's "Blue Steel" pose.
- The Matrix Reloaded (2003) -- The scene where the penguin hits a lot of foosas with a spinning wheel is a spoof with the scene where Neo hits a lot of agents Smiths spinning a stick.
- The Wild (2006) -- Parodies the trek from a New York zoo into the wild.
- Family Guy: Hell Comes to Quahog (#5.3) (2006) -- A man watches a parody of this in his Hummer.
- Zoo Tycoon 2: Extinct Animals (2007) (VG) -- A secret animal, The Killer Penguin (Hannibal Lecter-like penguin you get if you get a low score in the cloning mini-game) is based on the Agent Penguins in Madagascar, with ability of killing any other animals. In the info panel, it mentioned that it lived in Madagascar.
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