Also, a clip of Christian Slater's "You ever get the feeling..." speech from Pump Up the Volume is played at the beginning of Chapter 19, Act 2 as the club music starts playing.
Not to mention the graffiti on the alley wall that reads "Who watches".
Tales of MU is loaded with these — mostly to Dungeons & Dragons, the basis for much of the setting. After Gary Gygax passed away, a previously unnamed building was dubbed the Gygax Memorial Healing Center. Two of the funniest non-D&D examples that spring to mind are the in-universe equivalent of Occam's Razor, "Durkon's Hammer" (a Shout Out to The Order of the Stick) and Cat Girl Suzi asking, in broken "English", "I can has cheeseburger?" (a Shout Out to the LOLcatphenomenon)
And let us not forget the history class that was entirely devoted to making a "the cake is a lie" gag, in reference to Portal.
And the supplementary series MOAR MU had "I call it Vera" directly quoted, referencing Firefly.
KateModern features several Shout Outs to lonelygirl15. For example, Danielbeast is one of the webcam users hacked by Project Orwell in "The Leak", and the name "Bree" appears on Gavin's "PEOPLE I HATE" list in "The List".
Similarly, in "Straight To The Top", Gavin suggests that Lauren could audition for fellow Bebo show Sofia's Diary.
The first two chapters contain several allusions to The Matrix, both direct and indirect.
In Chapter 12, Jonas whistles part of the theme from The Great Escape before rescuing Reed.
Chromagic shouts out to a whole bunch of things. Mostly Pokémon.
On Homestar Runner, characters will do things like exclaim "What in Pete Sampras is going on?" or dress up as, say M. Bison or Jambi the Geniefor Halloween. One character, Coach Z, has the initials of Craig Zobel, who, along with Mike Chapman, wrote the original Homestar Runner children's book.
"Man, it's like the beginning of that game, except I don't have a gunblade, I got a broken sabre. Least Lenny can't fireball me, with like, kaPOW and stuff! Man, that would hurt." (The opening sequence of Final Fantasy VIII)
"Shit! SHIT! Injury! Medic! Somebody get me a potion! Who's on healing duty!? Critical hit people! Critical hit! With, like, the extra loud sound and red numbers and stuff!" (A general reference to the common healing item in the series)
Guy Rapide also mentions in passing having had a friend named Lucien Lachance. Other shout outs include catchphrases from Tengen Toppa Gurren Lagann, an adopted character suddenly talking like Kefka, direct quotes from films and games, visual tricks, namedrops, and sometimes characters that're slightly revised versions of one from some other media (the recent mod applications had a sample profile that was quite literally just a modernized Riku.) If one had the time and patience, an entire wiki could probably be dedicated entirely to documenting shout outs in Survival of the Fittest.
There are also tons of these (to other literary and artistic works) in the blog novelFartago. Just the ones I've caught: 2001: A Space Odyssey (the entire premise, that a monolith gives a tribe of cavemen self awareness, and they soon discover a bone can be used as a weapon), The Adventures of Huckleberry Finn and Don Quixote (the plot structure of two members of a society being outside their society and commenting on it), the writings of Sigmund Freud (the fact that the characters are motivated by their realization they will eventually die), Waiting for Godot (the writing style), The Unbearable Lightness of Being (Chapter 1: "The Unbearable Lightness of Cat Poop"), Superman and Batman (Flying Tago and Furry Night Bird Farta), The Lord of the Rings (Chapter 3: The Fellowship of Fartago), "The Treachery of Images" ("Zis Ees Not a Poop"), and those are just the ones I caught in the first three chapters.
Maddison Atkins features an episode called "Law & Order: Maddison Atkins". Adam can be seen playing Mario Kart 64 in one episode, and Maddison wears a Princess Peach shirt in another. With the possible exception of HTMLvis, all the pigeons' names (chosen by fans) appear to be shout outs: Trotsky, Mini Moon and Lady Gaga.
Stray is full of these. The story's Arc Words are an obvious nod to Planescape: Torment, Snake has a dog named Kaworu (Otacon chose the name), and there are more subtle references to Watchmen and Kafka.
The Whateley Universe is really a superhero comic book universe. So most of the buildings at Whateley Academy are named for famous writers and inkers of comic books. Schuster Hall, McFarlane Stadium....
There are tons of shout-outs in "Tales of the MCO, because the entire story is the protagonists watching an anti-mutant television show and MSTing the heck out of it.
The Phase novels are littered with shout outs, because Phase is a Deadpan Snarker with a lit background.
The first Phase novel has shout outs to the Bible, pointing out how Phase starts out as a pompous, spoiled rich boy. The chapter titles are Genesis, Exodus, Leviticus, Numbers, and Deuteronomy, and they metaphorically follow what happens to him in his first month or so as a mutant.
The third Phase story has chapter titles based on the twelve labors of Hercules, with references to those labors scattered throughout.
The sixth Phase story is "Ayla and the Grinch" which is an obvious Dr. Seuss reference for a Christmas story.
The seventh Phase story has chapter titles which are all biblical angels, since the A plot involves shoulder angels. Yes, shoulder angels.
The eighth Phase story has chapter titles from Spenser's "The Faerie Queene". Phase is that kind of person.
In a Let's Play of X-COM: Terror From The Deep, the Leviathian used to hit T'leth was named the Thunderchild. (A reference to Wells' War of the Worlds.)
Speaking of Let's Plays, B00n seems to have at least one Nasuverse reference per game he plays.
In the middle of this review of Genetos one reviewer suggests the possibility of a rogue-like shooter. Cue footage of... Microsoft Word... as a shmups engine... Naturally the player is an @ sign as a shout out to Nethack
