Throughout 3-2-1 Penguins!, there are a few references to VeggieTales. A piece of artwork used on a 2002 holiday catalog was also created, featuring Bob, Larry and Zidgel.
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- Trouble on Planet Wait-Your-Turn:
- Mrs. Conrad tells Michelle to apologize to Jason in a similar way to how Pa Grape tells Rosie to apologize to Tom in God Wants Me to Forgive Them!?!
- Michelle says that she and Jason stopped at Burger Bell on their way to the cottage, which is a reference to His Cheeseburger.
- Later, Larry the Cucumber makes a cameo appearance as a vacuum cleaner.
- Jason says "Listen to me!" when he gets everyone on Planet-Wait-Your-Turn to be patient with each other. This was also uttered by Junior in Rack, Shack & Benny and Archibald in Larry-Boy and the Rumor Weed. Michelle would also say this later in the next episode.
- Jason also says "No, no." when Zidgel tells Fidgel to wait his turn. This is the same thing Bob said in King George and the Ducky. Zidgel would later say this himself in Practical Hoax.
- The Cheating Scales of Bullamanka:
- Jason's line "Okay, okay." is a likely nod to one of Pa Grape's lines from Esther... The Girl Who Became Queen.
- Kevin says "Woah! Deja vu," which is a likely reference to one of Junior Asparagus' lines from The Gourds Must Be Crazy.
- When the Toad Roller approaches Fidgel, he asks "What is this thing?" This is the same thing Bob said when he first sees Larry's Suzy Action Jeep in Madame Blueberry.
- Michelle says "No wait!" when she convinces the Lizard King to play by the rules instead of cheating. This line was previously uttered by Junior in Where's God When I'm S-Scared? and Larry in Josh and the Big Wall!
- The Amazing Carnival of Complaining:
- Jason mentions The Pecking, which is a reference to Larry-Boy and the Rumor Weed, while playing pretend that there is a 40 foot chicken.
- Zidgel says "Did you say something?" to Midgel, which is a slight nod to what Archibald Asparagus asked Lovey in Larry's Lagoon.
- In The Shinin' Star Swing!, Bob the Tomato peeks through the Comet Lounge window.
- Runaway Pride at Lightstation Kilowatt:
- In Space Surfin' Superstar!, Kevin mentions Larry the Cucumber.
- Moon Menace on Planet Tell-a-Lie!:
- When Jason and Michelle are anxious to hear the rest of the story of their Granddad's dart championship, they say "What? What happened?" (a possible nod to one of Annie's lines from The Toy That Saved Christmas) and "What happened next?" (a possible nod to one of Bob's lines from God Wants Me to Forgive Them!?!), respectively.
- The Green-Eyed Monster:
- The Little Green-Eyed Monster including A Bigger version of this shrinks and disappears while Michelle and the Sheep on Picket deal with envy are Reminiscent to the Fib's Death by Junior's Truth in Larry-Boy! and the Fib from Outer Space!.
- Lazy Daze:
- Bert Bertman's cup has a picture of Larry-Boy on it.
- Midgel's sunscreen bottle has a picture of the sun from God Wants Me to Forgive Them!?!
- More is More:
- Jason mentions plunger-head does not qualify as a superpower, which is not actually true, considering Larry-Boy has this ability.
- One of the comic books Jason mentions that Kevin can read is Minnesota Cuke.
- Practical Hoax:
- One of Qwerty's original sounds is heard when Cavitus' screen shows the Federation Academy.
- Comedy of Errors:
- The way that Michelle got scared when watching a scary T.V. show is similar to how Junior Asparagus got scared before in Where's God When I'm S-Scared?.
- Later, Jason utters a couple of lines that were previously said by Archibald and Junior in Lyle the Kindly Viking: "That's not right." and "Thanks, guys."
- Sol also says "You've gotta be kidding me," which is similar to something Larry said in Gideon: Tuba Warrior.
- Wiki Tiki:
- Lance the Turtle is played several times throughout the episode.
- In the same episode, when the moon rock exploded, it turned into a piece of popcorn. This is a nod to the popcorn meteorites from The Gourds Must Be Crazy and Veggies in Space: The Fennel Frontier.
- Git Along Little Doggies!:
- Music from The Ballad of Little Joe and Moe and the Big Exit is used throughout the episode.