The Backloggery, a video game-tracking website, has badges for those who meet certain requirements in their collection. Having most of your games marked as beat earns the "Consider Yourself a Hero" badge (which resembles one of the power-ups from Contra as well), while having most of your games marked as complete earns you the "Master of Unlocking" badge.
Bee and Puppycat has a dream sequence in which a set of five puppycats are colored in the same color scheme as the first five Sailor Senshi of Sailor Moon.
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.
If you enter 'The Shire' and 'Mordor' and select walking directions, Google Maps will respond with a custom error stating "Use caution – One does not simply walk into Mordor.". See here.
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.
In Husbands the characters are talking about impulsive behaviour after Cheeks buys a dog on impulse.
Cheeks: "Well, being impulsive both got us really hot husbands."
Brady: "One time it also got be a tattoo that says "need more cowbell"." (slaps his behind)
Then, when Brady asks if they can get rid of the dog, Cheeks says that they've already imprinted and "done the whole Avatar hair/braid thing."
The "anti-walkthrough" website It He Software includes tons of shout-outs in its articles—to movies, obscure songs, etc.
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 Sofias Diary.
Napster Bad depicts James Hetfield as a hulking giant who tends to say "[something] BAD!" or "[something] GOOD!", in a reference to the "FIRE BAD!" line from Frankenstein (one of the shorts has James actually say "FIRE BAD!".)
"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.
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.