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 "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!!!"