The first film
- When caught at Grand Central Station, Skipper says, “We’ve been ratted out, boys!”
- Alex talks to a Basketball nicknamed "Spalding" with a muddy pawprint and face scribbled onto it.
- "You maniac! You burned it up! Darn you! Darn you all to heck!"
- "It's a cookbook! IT'S A COOKBOOK!!!''
- Marty graciously reminds zoogoers to "never spay or neuter their pets."
- The official poster is an obvious homage to the cover of the Wings album Band on the Run.
- Gloria asks the penguins where the people on the boat have gone; Skipper tells her "We killed them and ate their livers."
- The National Geographic Channel theme plays when Alex goes feral and attacks Marty.
- Melman rescues Marty from the fossa while swinging on a vine and screaming like Tarzan.
- At least two of the penguins are named after characters of popular science fiction films:
- Kowalski is named after Major Charles Kawalsky from Stargate and Stargate SG-1.
- Rico is named after John/Juan Rico from Starship Troopers
- Alex's Dream Sequence about steak falling from the sky is a homage to the sequence from American Beauty where Lester fantasizes about a naked Angela surrounded by rose petals on his ceiling.
The second film
- Mort acting like a gremlin on the plane's wing, and being initially identified as one, in a reference to Nightmare at 20,000 Feet.
- Again to Planet of the Apes, when Skipper says he's so happy at the monkey he could kiss him. Monkey: "All right, but you're just so darned ugly." and casually smooches him, to Skipper's surprise.
- The extended version of 'Big and Chunky' contains an aping of the chorus to Outkast's 'The Way You Move'.
