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Actor Allusion: In the beginning of the first movie, Alex's face while posing for a camera is the Blue Steel, the signature pose of Derek Zoolander.
His "surprise" face to Marty has been interpreted as a not to a scene from the same movie when Derek, covered in coal soot, jumps out of a dark corner to scare his father.
Marty's "black with white stripes or white with black stripes" conflict is an allusion to Chris Rock's own racially-themed comedy.
Actor Existence Failure: Bernie Mac, who voiced Zuba in Madagascar: Escape 2 Africa, passed away from complications of pneumonia on August 2008, a couple of months before the movie was released into theaters.
Doing It for the Art: One joke in the first movie required a million leaves to be created for it. One joke.
Dueling Movies: One of the most notorious example. The Disney-released The Wild had been in production for a few years already, but as was usually the case with their early films, DreamWorks caught wind of it and set out to (successfully) beat them to the punch. Madagascar became a hit and The Wild, finally released a year later, was immediately written off as a ripoff by those not in the know and just as quickly fell into obscurity.
In no other respects are the movies alike, but considering Europe's Most Wanted came out a short time before Brave, the scene where Julien, Maurice and Mort first meet Sonya and see her eyes glowing in the dark has a remarkable resemblance to Mor'du...
Fake Nationality: Various characters, especially in the third movie, are played by Americans putting on accents.
Originally only an instrumental version of "I Like to Move It" was to be used at the lemurs' party; Cohen then made up his own lyrics to the Reel 2 Reel song. The rest is history.
Animator Tom McGrath did what was supposed to be a temporary voice track for Skipper. Robert Stack was originally cast in the role, but after his death, Eric Darnell decided to keep Tom's voice in because he liked it.
What Could Have Been: Jennifer Lopez, Gwen Stefani and Madonna were originally considered to voice Gloria.
Melman was originally an okapi, but this was dropped in favor of a more familiar animal, the giraffe.
The Melman/Gloria pairing was originally going to be in the first film. Eventually, it was decided to leave it until the sequel, after the audience had gotten to know their characters.
At first, Gia was going to be a caged albino jaguar in the Monaco casino, and would have been freed by Alex.
In 2, Alec Baldwin was originally going to play a satirical version of himself who was tricking young actors into building a home/resort for him in Africa (claiming he was running an actor's studio). When this was dropped, they wrote the character of Makunga for him so he could still be in the movie.