In the credits gag of the first episode, Bloo is flipping through the channels, and finally decides on one. You can hear audio from Craig's earlier cartoon, The Powerpuff Girls, with the narrator saying his Catch Phrase.
Plenty of shout-outs to The Hitchhiker's Guide to the Galaxy as well, though. For instance, the villain from the video game Bloo plays is called "Lord Beeblebrox" and the two nerdy scientists who study Coco are called Douglas and Adam, respectively. Adam wears a blue t-shirt with the number 42 on it.
There's also a scene in the episode in which Bloo steals the Foster's bus which has a hitchhiker wearing a bathrobe holding a sign that says "Magrathea." In the same episode, there is a Star Wars shout out when Mac throws money for a toll out the window and misses to which Bloo responds "Negative. It only impacted on the surface."
In yet ANOTHER (much more obscure) Hitchhikers reference, the friends unite together to rescue a cat from a tree using what Frankie calls "Plan Z-Z-9-Plural Z-Alpha".
Frankie's t-shirt (that she wears 99% of the time) has a Stylized image of The Powerpuff Girls.
Similarly, in the episode where Eduardo gets fleas, the flea mayor looks and sounds strangely familiar.
In the pilot movie, whle Wilt, Coco and Eduardo are taking Mac and Bloo showing them allmthe imaginary friends, Mojo Jojo appears while Wilt is talking about "unimaginative friends" that kids just copy off of TV.
"Challenge of the Superfriends" begins with Tom Kenny's voice saying "The City", and ends with Bloo saying "Once again, the day is saved", and for a moment, Bloo adopts Mojo Jojo's speech patterns.
In "Destination Imagination", one of Frankie's potential replacements wears a t-shirt with a stylized picture of Mojo Jojo to parallel her own.
In a Halloween episode, Bloo turns white (he's sick) and everyone believes that he's a ghost. Coco picks up a phone:
Wilt: Who ya gonna call? Coco:Co Co-co! Wilt: They've been out of business for years!
Doubles as a Pac-Man reference. Bloo looks like Inky, and he turns into a white 'ghost'.
Also in that episode, when looking for the ghost, Wilt says, "That Phantom Menace!", namedropping one of the Star Wars films.
In "Dinner is Swerved", Mac and Bloo are opening doors along a hallway, one of which reveals a steam locomotive speeding right for them. They shut the door just in time, exactly copying a gag from Ringo's house in Yellow Submarine.
Affairweather Friends gives Barry a game console whose controller is awfully like the Wii's remote and nunchuk.
The pilot episode, House of Bloo's shows a Game Boy Advance in Mac's apartment.
In The Bloo Superdude and the Magic Potato of Power, the magic potato (in real life) is... a Nintendo DS—with mirrored button controls.
Foster's Home seems to have a Gamecube. It shows up in Fools and Regulations and Crime After Crime, among others.
Destination Imagination has a game level suspiciously like in the Mario games. Complete with snails replacing koopas, piranha plants, a growth item that comes out when Mac jumps under a block, and an item that makes Eduardo invincible for a short while (complete with power up music)!
A tall basket ball player named Wilt? C'mon guys, that's an easy one.
Quite interestingly, this basketball player also claimed to have sex with over 20,000 women...
Two of Coco's former owners who adopted her to research her look suspiciously like Dexter and Mandark, though their names are different, the concept and look is there.
Another from Destination Imagination is the big gem. It's a lot like the old Sonic games, where you feel accomplished winning the emerald and freeing a cute critter.
In the pilot movie, there's a bit where the now legless Extremasaur is chasing Bloo around the dump. It switches to an overhead view and looks like something out of Pac-Man. Not to mention Bloo's ghost shape. But why is Pac-Man chasing the ghost? Well he's Bloo isn't he?
The sequence of Jackie running through a suburban house trying to fend off his new family's cat in "Read 'Em and Weep" is an extended shout-out to Tom and Jerry, with several familiar gags. The lady of the house even resembles Mammy Two-Shoes.
The episode titled Squeakerboxx seems to be a shout out to the Outkast album Speakerboxx/The Love Below.
One of the biggest Shout-Outs to Video Games in Western Animation history: A chase scene in the pilot episode resembles the game Pac-Man to high degrees (which was easy, since Bloo looks just like one of the ghosts from this game).
Later, in "Destination Imagination", there's a longer scene that looks exactly like an NES Super Mario Bros. game, complete with Mac growing upon eating a... not mushroom, but pumpkin. The only real differences are said pumpkin and the appearances of some enemies.
Another shout out to Super Mario Bros. occurs during a chase scene, where a Sheet of Glass is being carried by two guys who are clearly Mario and Luigi.
In "Mac Daddy", when Bloo is trying to get rid of Cheese, he says to him, in a very sinister tone: "Wanna play a game?"
From Berry Scary: "He's the best, Jerry... the best."
In one episode, Frankie is basically saying that Mac needs to calm down. Bloo then adds, "Yeah, Mac. "Frankie says relax."
One episode features an imaginary creature similar to Pikachu, complete with lightning powers.
"Destination Imagination". The first clue thats something is wrong when the gang wakes up in the house, the carpet is the same as the one in ''The Shining". This pattern appears again at the hotel in "Pranks for Nothing".
At the end of "Bloo Superdude & the Great Creator of Everything's Awesome" a hallucinating Frankie imagines herself in a science fiction scene very reminiscent of Barbarella... a movie, it should be noted, that is very nearly porn.
His entrance to the stage mixes together aspects of the "Stonehenge" and "Alien" scenes from This Is Spinal Tap.
Pizza Party's album/single CD cover is a parody of Bruce Springsteen's Born in the U.S.A—a shot of a guy wearing pants from behind, Springsteen's cover with a pocket holding a hat, Pizza Party's with a slice of pizza.