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troperville

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.
Or in a recent episode, where Chowder made the least subtle but most awesome reference to Portal ever, by saying "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.
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". For example, Shnitzel's samurai outfit is the yellow-black striped outfit from ~~Kill Bill~~ Bruce Lee's Game of Death, 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.
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 "Big Ball" ^or "Field Tournament Style Up and Down On the Ground Manja Flanja Blanja Banja Ishka Bibble Babble Flabble Doma Roma Floma Boma Jingle Jangle Every Angle Bricka Bracka Flacka Stacka Two Ton Rerun Free for All Big Ball", the giant turtle resembles Bowser.
- The referee shouts "GOOOOOOOOOOOOOOOOOOOAAAALLLL!!!"
The Dancing Diablo peppers resemble the Jalapeno is Plants vs. Zombies.