- One of Rico's tasks that he has to perform get rid of his "curse" in "Misfortune Cookie" involves being slapped with fish.
- In "Eclipsed," Kowalski analyzes Julien and says, "I'm picking up good vibrations."
- There's a rather long-winded piece of dialogue which ended up referencing, of all things, the song "My Girlfriend Who Lives In Canada" from Avenue Q, even going as far to mention that said girlfriend is a lie.
- Also, how many Alices it would take to make her useless? 42. And Agent X.
- Manfredi and Johnson, the two characters Skipper mentions on occassion, are the names of the prisoners killed in the opening of Stalag 17.
- During the Falling-in-Love Montage in "The Falcon and the Snow Job", Skipper and Kitka mold pottery together.
- The penguins' car has a New Jersey license plate reading "I [heart] BNJVI."
- In "Over Phil," Mason walks in front of a profile of himself and says "Good evening," referencing the opening of Alfred Hitchcock Presents.
- The "Jiggles" episode is a Shout-Out to Flubber and The Blob (1958).
- In "Stop Bugging Me," Kowalski and Skipper are playing Twenty Questions. Kowalski asks, "Is it bigger than a breadbox?"
- In "Work Order", the penguins are up against a giant Russian man who loves his sandviches.
- In "Otter Gone Wild", a now feral and strong Marlene carries Julien to the top of an obelisk where she has to fight off the Penguins in remote-controlled biplanes.
- When Julien loses his groove, Skipper asks him "So you think you can't dance?"
- In "Operation: Blowhole" Kowalski's reaction to Chrome Claw (A giant lobster with well, a Chrome Claw) "That would be extremely impressive if weren't about to-*Smacked*. Which admittedly is more well-spoken than the original version.
- "Lemur See, Lemur Do" starts with Julien finding a crate in a way closely resembling some apes finding The Monolith. There's even the music.
- That same episode, Julien refers to the robot as his BIONICLE buddy.
- From Friend-in-a-Box:Skipper(looking into viewfinder): "I got my eye on some kid and his beagle in a pumpkin patch. What a blockhead."
- To their own Christmas Caper special in "Hello, Dollface". Some guy picks up Private and squeezes him like the crazy lady, Private poots like in the special and the dude says, "A talking penguin? What is this, 2005?" 2005 being the year that short was made.
- Brief mentioning of Animal Farm in "Mr. Tux".
- "Skipper's log..."
- "Do a barrel roll!"
- Joey doesn't share.
- In "Jungle Law", at one point, Bada and Bing, the resident gorillas of the zoo, ride around on rhinos armed with barrels.
- In What Goes Around Officer X drops the infamous "You shall not pass!" from Lord of the Rings.
Shout Out / The Penguins of Madagascar