- Oh so much video games especially Katamari Damacy and Super Mario Bros.. (twice. Two Captain Ersatzes of Mario and Luigi show up in one episode and an oversized Bowser shows up in another) being two obvious examples.
- In "My Big Fat Stinky Wedding", where Chowder made the least subtle, but most awesome reference to Portal ever, by saying "But I was promised cake! The cake was a lie!"
- One of the Halloween episodes was a parody of The Exorcist, and the other contained a shout out to Psycho at the end with Gazpacho in a birthday suit.
- In "The Arborians" there is a brief shot of Shnitzel playing a synthesizer, wearing a yellow raincoat and an Energy Dome.
- When Chowder is possessed by the Poultrygeist, he starts insulting Mung, telling him that "Your mother was a polar bear! Your father was a figure skater!" and telling him that he smells of flour and cheese.
- When Mung Daal recounts the time Truffles tore off his beard, leaving only the famous mustache, Chowder whispers: "She broke the combo?".
- By far, the greatest collection of Shout Outs in one episode is the episode "Tofu Town Showdown", which is pretty much the writers challenging each other to cram as many references to kung-fu films and shonen anime within the span of 11 minutes. For example, Shnitzel's samurai outfit is the yellow-black striped outfit from Bruce Lee's Game of Death (which is more popular as what Uma Thurman's The Bride character wore in the Kill Bill movies), Chowder sings a pastiche of "Eye of the Tiger", Shnitzel wins the final battle by going SUPER SAIYAN, and finally, "RAHDOKEN!!"
- Similarly, in "Weekend At Shnitzel's", there's a fight scene that takes a lot of cues from Street Fighter, including a recognizable Hurricane Kick, Shoryuken, Hadoken, and Flash Kick. Plus a Mortal Kombat-style demand for a Finishing Move: "Get 'er done!" as Shnitzel is knocked down.
- Mount Fondoom, "YOU SHALL NOT PASS"... they really like taking on LOTR. And Dwight Schultz does a terrifyingly good Gandalf.
- That line makes a return in "The Sleep Eater" with Mung slamming a giant fork into the ground a la Gandalf.
- Gazpacho's surreal dream sequence in "Gazpacho!" is a subtle not to the video for "Don't Come Around Here No More" by Tom Petty (complete with Gazpacho's body made out of cake and everyone dressed as Alice in Wonderland characters).
- Not to mention Souron.
- Back before Chowder first aired, C.H. Greenblatt expressly stated how much Katamari Damacy inspired him in the creation of this show. The King of All Clouds (Sky?) is intentionally based off The King of All Cosmos, as well as the entire Grubble Gum episode.
- In one episode, after Chowder unearths a sugar sapphire, Mung tastes it. He has a seizure, shaking his head about, before it spontaneously pops to Bubbles' head saying "Aww, that's sweeet!" as part of the theme song is played.
- "I can only count as high as 42. How high can you count?"
- In "The Hot Date," one of the character is waiting at a fancy restaurant for the titular hot blind date, who is very late. At one point, Ms. Bellum from The Powerpuff Girls shows up looking for her blind date (complete with the Powerpuff Girls theme playing in the background), having been delayed due to a monster attack, only for her date to be someone else.
- In "Big Ball" or , the giant turtle resembles Bowser.
- The referee shouts "GOOOOOOOOOOOOOOOOOOOAAAALLLL!!!", like in latin soccer.
- The Dancing Diablo peppers resemble the Jalapeno is Plants vs. Zombies.
- There's even a reference to Alien in the episode "The Meach Harvest." One of the guard meaches roars and sticks out its tongue, which has a mouth on the end of it. It's even credited as "Alien Meach."
- In "Sing Beans", the on-edge customer waiting for his order strikes a very clear resemblance to the Lion from The Wizard of Oz, especially in voice.
- Sour Ron from "The Puckerberry Overlords" is a play on Sauron.
- The live-action car wash sequence from "Shopping Spree" is accompanied by an instrumental disco song that sounds like the theme song from Car Wash.
- The Apprentice President from "Panini For President" is equal parts John F. Kennedy and "Diamond" Joe Quimby, which is itself rather amusing since the latter was partially inspired by the former. He has Quimby's nearly spherical physique, Kennedy's Irish red hair and their mutual exaggerated "New Yoak" accent.
Shout Out / Chowder