"Pants in Space" is a pun on the classic Muppets sketch, "Pigs in Space".
Another King Kong reference is made, when Jake calls Windsor "Baby Kong".
And another Abbott and Costello reference, when Principal Pixiefrog first meets a man named, "I Didn't".
"Docu Trauma" has Adam chased around by a documentary filmmaker named Zira Cornelius, and the whole episode is basically a massive shout out to the Planet of the Apes franchise.
In "Sick Day", Adam Lyon is absent during role call, leaving Mr. Hornbill saying "Lyon, ... Mr. Lyon, ... Adam Lyon, ... Lyon, ... Lyon" for a while. This is a reference to the famous "Bueller" scene from, "Ferris Bueller's Day Off".
Adam plays a video game system called "Game Circle", which is a parody on Nintendo's Game Cube.
In "The Spiffanos", The Spiffies are modeled after The Mafia, with ringleader Phinnius Porpoise doing a very good impression of Don Vito. They even call him "The Finfather".
Also, when Marvin Hammy rode up to Adam and Jake on a tricycle, this was a reference to The Shining.
Let's also not forget how the title of the episode is a pun on The Sopranos.
In "Diplomatic Insanity", yet another King Kong reference is made, when Windsor's species label is given as "Kingus Kongus".
In "Gorilla My Dreams", Principal Pixiefrog calls out in misery, for his ex-wife Lenore. He shouts "LENORE!" out the window, and a raven crashes into the window panel. This is a reference to Edgar Allan Poe's The Raven.
Windsor compares Principal Pixiefrog to a modern day Ashton Kutcher. note In the original storyboard, Windsor compared him to Randolph Scott. I guess this was changed to a reference the kids would get.
In "The Morning Zoo", Adam, after been hit on the head by a piece of concrete, became Joey Mack.
In "Meet the Spidermonkeys", while acting out as a zoo animal and dealing with the patrons, Adam says "Just smile and wave".
In "The Hyena and the Mighty", Mr. Mandrill does some standup in the same fashion as Jerry Seinfeld from Seinfeld.
The episode title, itself is a reference to "O. Henry", the pen name of William Sydney Porter.
In "My Feral Lyon", Adam causes a distraction in the school, by running through the halls and singing "[[The Breakfast Club I wanna be an airborne ranger!''".
In "A Mid Semester Life's Dream", we get tons of these.
First of all, note the title pun.
Mr. Hornbill makes a reference to the original Batman show.
Miss Chameleon teaches her class about Shakespeare.
Charleston Festoon is a parody on Charleton Heston.
Windor quotes JFK and Jake quotes John Donne.
In "The Ivy League", Mrs. Warthog watches a show called "Seal or No Seal".
In "Robo Frog 3000", we get references to Robo Cop.
In "The Notorious Windsor Gorilla", which is a reference to "The Notorious B.I.G.", Adam paints a picture, reminiscent of Margaret Keane's Big Eyes paintings.
Captain Corporate says that he's the very model of the modern middle management.
Principal Pixiefrog and Windsor do a parody on "Inside the Actor's Studio".
In "Ingrid Through the Out Door", Principal Pixiefrog dresses as Groucho Marx.
Mr. Hornbill teaches the kids that rubbing mud on yourself will prevent predators from being able to see you. The camera shows a cartoon Predator sitting in a desk, who says, "It's true."
In "A Whole Zoo World", when Adam tries to capture Jake while jumping off a waterfall, he shouts, "PREZENKOWSKI!" A reference to executive in charge of production for Cartoon Network, Jeff Prezenkowski.
"Animal School Musical", while mainly being an obvious High School Musical parody, contains a few more references.
David Coppertrout dresses up as Jeannie, from I Dream of Jeannie, during his musical number about wish granting. The writers must have mixed references, since when granting the wish, instead of crossing his arms and bobbing his head, David twitches his nose like Sabrina from Bewitched.
The Monty Python's Flying Circus Monty Python Foot makes a cameo, during "Waiting in the Wings", stepping on James Ant. Additionally, a hand drawn in the same style is also used, having James perch on it's finger.