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.
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!
Also in that episode, when looking for the ghost, Wilt says, "That Phantom Menace!", namedropping one of the Star Wars films.
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.
2 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.
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?"
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.