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I was watching Fosters and some people were throwing tomatoes at Bluu and he says, "Attack of the killer tomatoes!" ::shakes her booty '80s style::

In one Strong Bad email, they used the phrase "everybody put their weight on it." "Put your weight on it," is a registered trademark of Rudy Ray Moore.

And speaking of Rudy Ray Moore...
Professor Farnsworth: Dolomite, the baddest element of them all...
Bender: I'm 10% Dolomite!

There was a Josie in the p***y Cats parody in Fairly Odd Parents.
Danny Phantom mockingly calls one of the bad guys "Captain Kid," which is the name of an old movie short series and comic strip.

In GTO, Onizuka gives one of his students a Cutey Honey outfit, and she gets hit on by creepy otaku. GTO once dressed up as Devilman. There is Lupin IV slot machine in one episode.
When the kids were stealing the test results, with mask of politicians (one was Kennedy):
-We've got the mugs of politicians and the hearts of Lupin!
-~Lupin the third~

There was a time when I didn't know who Ultraman was. Then I watched GTO and Simpsons in the same day, and both had Ultraman references. GTO has too many Ultraman references to name them all, but I've seen two in Simpsons. In one, Ralphie just says "I'm Ultraman."
In the other, a guy is making a documentary and is interviewing the hall monitors. Millhouse is talking about how hard it is to be a hall monitor, then Ralphie says "My shash says 'Ultraman,'" and he starts making shooting noises.
There is an Ultraman parody in South Park as well. Barbra Strisan (sp) was becoming a monster and one of the guys that tries to fight her is dressed as Ultraman, one of the others was a villain from Ultraman.

There is one episode of Dexter's Lab that is entirely a Speed Racer parody. "I'm Dexter's sister Deedee who died in that race, except I wasn't dead..."
Dexter's also has a parody of the Ed's computer (Cowboy Bebop). It was a little yellow face and it kept saying "Konwichiwa."
A Pokemon parody in Johnny Bravo, called "Clam League 9000":
"You sacrifice plot development for cheap action and merchandising!"
"And you can be a winner too if you go to the store and buy our toys, buy our toys, buy our toys!"

In one episode of Looney Tunes, they make reference to the "film" Jungle Jitters, which is actually an episode of Looney Tunes on the Censored 11, for portraying Africans as cannibals (even though cannibals do still exist in remote parts of Africa.)

Make me happy and tell me all the esoteric references you've seen. scream

I just thought of something, in Calvin and Hobbes there's this one part where Calvin makes his hair just like Astro Boy . Does that count?

Damn, where do I start?

- In JLA/Avengers, Superman says to Thor "Our dials go to eleven", which is a roundabout reference to "Spinal Tap".
- Dash's hair in The Incredibles wa taken from Pietro "Quicksilver" Maximoff, one of the Avengers and the son of Magneto.
- Elastigirl is the name of one of the members of the Doom Patrol.
- The "Gameslave 2" episode of Invader Zim opens with a parody of Vampire Hunter D.
- The "Megadoomer" episode of Invader Zim is a blatant parody of Neon Genesis Evangelion.
- The Go Go Yubari character in Kill Bill is a homage to Battle Royale.
- The Bride's tracksuit in Kill Bill Volume One is based on the one that Bruce Lee wore in his final movie, "Game of Death".
- Bill's speech about Superman in Kill Bill Volume 2. He's referring to the Pre Crisis Superman.
- Spider Jerusalem's appearance at the beginning of Transmetropolitan has been suggested to be based on reclusive author Alan Moore.
- The relationship between Spider Jerusalem and The Beast is based on Hunter S Thompson and Richard Nixon
- Spider Jerusalem's regular appearance is quite possibly based on either Grant Morrison or The Invisibles' King Mob, who is based on Grant Morrison.
- The Smiler's campaign slogans are slightly altered slogans used by George W Bush and Tony Blair.
- There is an allusion to the Kent State Massacre in which the National Guard opened fire on student protestors in Transmetropolitan.
- The button that Spider Jerusalem wears is likely a subtle reference to Watchmen.
- The Second Rennaissance in The Animatrix uses several chilling allegories including Tianamen Square and the Vietnam War.
- Episode 5 of FLCL is rife with parodies including John Woo movies, extensive Lupin 3 references and a parody of the South Park animation style.
- Both Bulma in Dragon Ball and Haruko in FLCL have dressed as Playboy Bunnies as they appeared in the Chicago bar in the 60's.

Round two.

- John Constantine was created by Alan Moore when the artists asked him to make a character that looked like Gordon Sumner (Sting). He is now arguably the best known character from DC's Vertigo imprint and his solo series has over two hundred issues.
- Dream from Neil Gaiman's Sandman is said to be based on the not fat Robert Smith of The Cure fame.
- Deadpool was originally created by Rob Liefeld and was a transparent plagarism of DC's Deathstroke, who's real name is Slade Wilson. Deadpool's name is Wade Wilson.
- The Teenage Mutant Ninja Turtles began as a drunken parody of Frank Miller era Daredevil sketched on a cocktail napkin.
- In the fifth episode of FLCL, Haruko yells "Daicon 5", which is the name of the convention where the founders of Gainax met.
- In the sixth episode of FLCL, Naota's father alludes to the statement by the creator of Gundam that it was "just a giant robot anime", much like what Richard Adams says about Watership Down.
- In the recent Cutey Honey OVA, a combined parody of magical girl transformation sequences and Osamu Tezuka's Astroboy appears in the form of "Penisman".
- A cat by the name of "Rhett Butler" appears in the first season of Sailor Moon. Rhett Butler was Clark Gable's character in the movie "Gone With The Wind".

In one episode of Fairly Odd Parents, there was a parody of Captain Planet, Foxy Popeye and other various Golden Age cartoons. There was even a street sign that said "Ub Irkewerks." Best. Episode. Ever.

One episode of Danny Phantom had a MPORPG that may have been supposed to be a .hack parody, but I'm not sure. Another episode had a Hello Kitty parody though.

Some of Miyazaki's films have tributes to Monkey Punch in them. On the truck in Kiki's Delivery Service, it says "Monkey," and somewhere in Porco Rosso it is supposed to have Monkey Punch in hiagram.

A recent episode of Justice League: Unlimited had Wonder Woman changing into her costume with a pirouette, just like was done in the WW live action series from the 70s.

I don't know if this counts..

But in King of the Hill, when they go to Japan, Bobby places something that has the gameplay like the DDR games and others like it.