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 anime. 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!!"
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.
"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 "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!!!"