Pretty much anything with a name in Eureka Seven is a reference to something, usually music-related (with American cinema being the next most frequent source). This includes episode titles, which, except for one, are all song titles...
...which is nothing compared to Bleach: While the actual series keeps musical references to a minimum, every chapter title since the series began is either the title of a song, the name of a band, or a line of lyrics, usually slightly modified. Bear in mind that as a Long Runner, Bleach is well over 500 chapters long, meaning it has at least that many musical references.
JoJo's Bizarre Adventure is absolutely packed with references to music that's popular in the west. Some of the most referenced sources in the comic include The Beatles, Pink Floyd, Led Zeppelin, AC/DC, Queen, and Prince, just to name a few. That's not even getting into the other bits of western popular culture and all the homages to Italy that are littered throughout the work.
Watchmen has a whole load, especially musical references, but also to works of literature and to modern (1980s) pop-culture.
Astérix as well, but like in the Looney Tunes example, some are too old to be recognized, even by the French audience.
The League of Extraordinary Gentlemen. Specially in the latest graphic novels. Seriously, you will be surprised how many British 60's sitcom characters can appear in a number of pages. It wasn't until the third series that there was an original speaking character was not absconded from an earlier work (even background characters running from a battle were Fagin, Dodger, and company), and that original character was Champion Bond of her majesty's secret service.
And also Alan Moore's Top 10, which came out at the same time as the early installments of Lo EG. Practically every background character, business name, vehicle or grafitto is a shout out to someone or something.
As you can see in the picture above, the Monica's Gang comic can get so blatant and ridiculous in it's shout outs, it can be called Refuge in Audacity (and that Avatar parody manages to put more blue characters - which include a real person, Zinedine Zidane, if only by putting him in the French team kit... - in another panel◊). This also applies to other Brazilian comics, such as Holy Avenger.
A Running Gag on a satirical Tumblr about Monica's Gang is saying "Mauricio's lawyers, get ready..." every time the comic uses No Celebrities Were Harmed. (the caption of the page image was "that panel alone is probably worth two billion in lawsuits, dammit!")
Bloom County was awash with pop culture references and celebrity mockery... largely because those beguiling assets were virtually absent from the comedic media at the time. But just look at us now. No, it's not my &@%# fault.
This can actually be quite a problem in fanworks, especially since (a) the authors are generally pretty geeky by default, (b) there's often an unusually large amount of interaction between writer and audience, and (c) they're derived from pre-established settings anyway. Eventually, the sheer quantity of Shout Outs to other shows can reach critical mass, causing a hitherto coherent story to collapse into a formless heap of references.
A conservative estimate of Battle Royale fanfiction 72 Hours' reference count would be 500. This is not an exaggeration, considering that each of the eponymous hours has its own chapter, and it's roughly equivalent to a 1300 page book in length. It is, however, testament to the obsession with shoutouts held by the author.
A dark humor Harry Potter fanfiction by Virginia Riddle-Malfoy on fanfiction.net Ginevra In Darkness uses a lot of characters from other series - particularly the renamed Integra from Hellsing and has cameos of other characters such as Sherlock Holmes and John Watson from the BBC Sherlock, Sarah Williams from Labyrinth, Adam Young from Good Omens, Darian Shields from Sailor Moon, Daria. Also uses quotes from Buffy, Batman, and A Very Potter Musical. She manages to keep to the plot, but seems to amuse herself by seeing how much she can slip past the readers without getting caught. 
Another fanfiction by the same author Harry Potter and the Turn of the Tides uses the Halloween hijinx trope and crosses over for a single chapter Harry Potter, Sailor Moon, Megas XLR, Buffy the vampire slayer, Star wars, Indiana Jones, James Bond,Ranma, Lordofthe Rings, and Monty Python and the Holy Grail. The fic unfortunately was done by the author in high school, and she rightly abandoned it as the tropes written about became far too overdone and dull. Still worth a plug for excellent characterization. 
Here's a fun Drinking Game: Take a shot every time you spot an allusion or reference in My Little Mission: Sneaking is Magic to something from the Metal Gear Solid series. You'll be hammered by the fifth chapter. The author manages to pack dozens upon dozens of references to the series into the fic, often going out of their way to do so.
Or the "_____ Movie" parody series in general (Epic Movie, Date Movie, Scary Movie...), in that they are nothing "but" pop culture references and shout outs, without the film makers remembering for a parody the reference has to be the start of the joke, not the end of it. They do at least manage to integrate the references into the movie's action, however, if only for a cheap slapstick gag.
Any Quentin Tarantino film. Cracked calls him less of a director and more of a movie DJ, treating shots, characters, and plots like music samples.
A Series of Unfortunate Events: If you made a list of every time Snicket makes a Shout-Out to literature and history in one of the later books (especially through Sunny's dialogue), it would be almost as long as the book itself.
Ready Player One has this as part of its plot, but narrows it to 1980s video games and pop culture in an effort to solve the puzzle left behind by a rich eccentric as part of his will.
The works of Philip José Farmer are sometimes Reference Overdosed, particularly those set in the Wold Newton universe. A single work may be a Homage to one writer while encoding allusions to the work of many, many others. For example, no name is innocent until all anagrams, obscure linguistic derivations and so forth have been exhausted.
Most stories by Kim Newman (including those written under his Jack Yeovil pseudonym), especially the Anno Dracula series.
The Ciaphas Cain books are absolutely loaded with references to both science fiction and turn-of-the-century juvenile adventures.
The author of the Warhammer novels collectively known as "The Vampire Wars" acknowledges his books contain at least a hundred references to classic vampire stories like Dracula. One of his fans sent him a list of references in his novels, but the author didn't have the heart to say he'd missed about another fifty.
The first page of Where's Waldo? The Wonder Book. It puts all the other examples to shame.
Bret Easton Ellis likes to do this with his characters to highlight how shallow they are. Many pages in Glamorama are just long lists of Victor and his friends name dropping celebrities, and in American Psycho, Patrick has to describe in excruciating detail what everyone is wearing.
T. S. Eliot's works, especially The Waste Land. The poem is full of classical literature and religious references, and quotes them in their native language.
Zadie Smith's White Teeth contains tons of references to various minutiae from literature, history, science, and pop culture (both British and American). Some of them serve almost no purpose, such as a Long List of all of Millat Iqbal's favorite books, records and tapes, and movies on videocassette.
Monty Python's Flying Circus: many encyclopedic references to historical and cultural figures, exotic animals and places. Most of these jokes could make sense to intellectuals, but then there are also many references to British culture, especially politicians, TV hosts and programs that were famous during the late 1960s and early 1970s. They are usually completely incomprehensible and obscure to international audiences and even to the English, especially while Time Marches On.
Mystery Science Theater 3000. Being a show built around providing audio commentary to Cult Classic genre movies, it couldn't help being stuffed full of references, but some of the references were so obscure only the members of the show's own cast understood them.
Supernatural, particularly when it comes to music. Almost every episode from the first 5 seasons is named after a classic rock song, while the newer episodes reference other.
Red Dwarf often makes reference to films such as Casablanca, Gone with the Wind, and Blade Runner. For instance, the episode Back To Earth is considered by most to only be enjoyable if you know the Blade Runner references, to most other fans it is a horrible episode.
We don't even try to list the shout outs in Farscape. Crichton is a fountain of late-20th-centrury cultural references, which only makes him a Cloud Cuckoolander in the eyes of all the aliens around him.
The Tau'ri (Earth-born humans) in the Stargate Verse pretty much have Genre Savvy as their Hat. They're well aware that their daily lives resemble science fiction and are all too happy to show it.
Also, Ghostface Killah had a song from the 1996 album Iron Man (which was when he started using the alias Tony Stark) entitled "Daytona 500" (named mostly for its fast pace) which used clips from the original Speed Racer to make one of the first Anime Music Videos which is still considered a favorite by many.
The song itself contained samples from Bob James' "Nautilus" and "Crab Apple" by Idris Muhammad whle the chorus from "Turn The Beat Around" by Vicki Sue Robinson sped up and reworded for the hook. And even featured two samples from previous Wu singles, "Mystery of Chessboxin" and Raekwon's "Incarcerated Scarfaces" which also had an obvious Shout-Out in title as well as the lyrics.
John Cena and Tha Trademarc do a lot of this on You Can't See Me; ironically, most of the references are not to Professional Wrestling. This was spoofed in their video for "Bad, Bad Man", which had as its plot a homicidal maniac kidnapping Madonna, Michael Jackson, and certain other 1980s cult figures - not to mention that said homicidal maniac was played by Gary Coleman. And Cena, Trademarc, and Bumpy Knuckles dress up like (respectively) Hannibal Smith, Murdock, and Mr. T from The A-Team!
Half Man Half Biscuit. Their website has a section dedicated to explaining some of the references.
No More Kings. When describing them most places refer to them and funk/pop mixed with 80s references. Though there are more references, the 80s are just the most prominent.
Frank Zappa: his music was deeply personal and references several aspects of the society of his time, including music, commercials, politics, TV and even inside jokes in his own band and anecdotes from his own life. Zappa once claimed that he doubted if his lyrics could make sense to anyone but himself.
Sage Francis, a rapper from Providence, RI, makes tons of references to "classic" hip hop songs. He'll often re-use classic lines, substituting a word here or there or reversing the word order as a kind of wordplay homage; he'll also re-use the cadence of certain iconic lines in a subtle nod.
R.E.M.'s music would frequently make references to ancient mythology in order to conceal the true meanings of the songs (namely Michael Stipe's bisexuality or political events). This had the side effect of making people think he spoke gibberish. To clarify, the first time he admitted to writing a song with straightforward lyrics was in 1992 when the band recorded "Everybody Hurts" - 12 years after they started.
Warhammer and Warhammer 40000 are packed with shout-outs, and it's not just the historical or literary origins of practically every faction and variant army (especially Space Marines and Imperial Guard). The flavor quotes, maps and locations, character names, most of the fiction, and the universe backstories are plundered from all over, ranging from the Bible to minor quotes from travel writers.
NetHack is quite possibly the most reference overdosed game to ever be created. It boasts hundreds of literary quotes regarding topics as mundane as doorways and a wide reference pool that encompasses a large variety of topics: ancient mythology, fantasy, geek culture, mathematics, physics and other games.
World of Warcraft originally used to have a handful of Shout Outs in the form of traditional Easter Eggs, but since Burning Crusade, almost every character, quest name, and area is a reference to something, probably blatantly.
Touhou. Even the attack names can be references to Japanese mythology, and obscure ones at that. One game had a plot that referenced three separate Japanese myths...and UFOs. It also had references to older games in the series and Space Invaders.
Meat Boy games. From chapter intros to level titles.
Retro City Rampage features tons of Shout Outs to not just old-school games, but movies and TV shows as well. The introductory mission of story mode features references to Batman, Ducktales, Teenage Mutant Ninja Turtles, The A-Team, and Bill and Ted's Excellent Adventure in rapid succession.
Aqua Rhapsody, The developer notes that a lot of small things are "shoutouts" to video game, anime, etc. These are as obscure as the level transitions that fade out in a similar manner to Space Harrier.
Part of the fun in Skullgirls is trying to find how many references to anime, manga, and other video games you can find. Peacock in particular makes up so many of the Shout Outs that she could be considered Reference Overdosed in her own right.
The Adventures Of Massmouth series is filled to the brim with references; entire lines are quoted verbatim, names of locations and characters in pop culture feature heavily, not to mention that all the enemies are basically ripped from other games and given different names.
Revenge of Shinobi has a lot of pop culture characters as bosses. In the re-release, some of them had to be censored or changed. Here's a dialogue in a youtube comment section:
sandwichoftruthiness: So you're a ninja and so far you've fought Rambo clones, Terminator-Hulk, Spider-Man, Batman and Godzilla. Did Sega's CEO just write some fan-fiction and tell them to make it into a game? slowbeef: Does the "Tropes vs. Ninjas" title make sense now?
Freefall: For the most part the numerous references to a wide range of concepts are worked into the storyline of this Webcomic Longrunner well enough that they're not jarring, though occasional references to 20th/21st century pop culture phenomena roughly five centuries later (as per Word of God on the forums) can sometimes seem a little odd to some readers.
Nullmetal Alchemist is also worth mentioning in that it parodies the very idea of having references. Ed specializes in Contextually Insensitive Magic, and frequently deliberately cuts from the show to an out-of-context clip of another video to distract and/or annoy his enemies.
Rose: I don't understand, how did you defeat him using karaoke?
Ed: The guy had a rational hatred for references; a vocal cover was too much for his elitist brain to handle.
This phenomenon was a constant in the Global Guardians PBEM Universe, and given that the players involved included ordained ministers, a professor of quantum physics, a member of the British House of Commons, several professional writers, a television producer, a movie special effects expert, a chef, three lawyers, active duty soldiers, artists, actors, attorneys, doctors, nurses, police officers, fire fighters, a librarian, a stock broker, computer programmers of various types, a Roman Catholic priest, a biochemist, the mayor of a small Florida, and a professional dominatrix, amongst others, all of whom were highly educated and all of whom were widely read, this was to be expected. Some stories were so thick with various references (from pop-culture to legal to scientific to political) that the story itself was lost in the mix.
Everything about it, since it's a superhero universe which has Marvel and DC as superhero comic publishers within it. People constantly refer to this, talking about a girl who leaps in front of teammates to protect them as having 'superman syndrome' or arguing about what is needed for Marvel to make an Iron Man movie or even talking about why 'real' supers can't swipe copyrighted/trademarked superhero names.
The Phase novels are chock full of literary references, which even touch the chapter titles and Phase's obscure jokes that no one else gets. Generator is more likely to make references to anime and cartoons.
Survival of the Fittest: Due to being a collaborative work between the board's members, it qualifies. While there have been Shout Outs to previous versions and the original canon, a few others are to... less expected works, such as a character suddenly talking like Kefka, and a few characters being an Expy of characters from other works. Honestly, if one were to list every single reference in SOTF, it would take a while. It has been a minor issue on the board, however, in how many Shout Outs are okay.
Family Guy, although it has gotten out of hand for a lot of fans, and nowadays the show frequently includes references that are nothing but padding, without a joke to justify their inclusion. It's gotten to the point where you could type practically any pop-cultural phenomenon of the past 80 years into the YouTube search engine and find a Family Guy clip spoofing it.
Many Looney Tunes and Tex Avery cartoons, but as Time Marches On fewer and fewer people get the references. This is especially caused by references to film actors, radio shows, songs, and commercials that were very popular in the United States during the 1930s, 1940s, and 1950s, but are nowadays completely obscure for modern audiences. Examples are:
"Turn off that light!" (reference to air raid wardens during World War II)
Transformers Animated. Without interfering with the plot or making it so that you can't follow it if you don't know what's being referenced, it manages to fit in a zillion little easter eggs into every episode. Its "Allspark Almanac" guidebook is this taken to its logical extreme. Every single thing references something, no matter how deeply the reference is buried note Some of the symbols on some pages are actually from the Cybertronian language as seen waaay back in Beast Wars, and are references to movies, songs, etc. Ironically, the references written in Cybertronix primarily reference everything but TF itself. or how obscure the things being referenced are note For example, a minor character from a Japanese radio program, the letters page of a comic book from 20 years ago, or a not-official TF comic serial printed in a magazine might be name-dropped, and items whose composition isn't mentioned in-show will be given as materials that one side or the other tried to obtain in a G1 episode or comic. Basically, if it's a number or a proper name, it references something. No exceptions. Period. Oh, and a second volume is on the way.
The short-lived Spaceballs series was nothing but Whole Plot References. No original storylines or jokes to be found anywhere. Probably explains why it was short-lived. Yes, the whole concept is a Whole Plot Reference to Star Wars, but you'd think the writers could come up with at least a few new plots and gags in the 15+ years it took to get the cartoon made.
South Park series have tons of these in almost every episode.
The Imaginationland episodes of South Park, which feature virtually HUNDREDS of fictional characters.
The Venture Bros.. The show references music, history, art, literature, politics, pop culture (from the 1890s through modern), comic books, pulp fiction, film, television, philosophy, religions, etc. Each episode is approximately 22 minutes long and every single one includes dozens of these.