Link makes one to EarthBound in the beginning of Chapter 27 of the first story, when the group receives Skolar's Star Power.note Which is Star Storm, which is Poo's most powerful move.
Link makes one to Pikmin in Chapter 17 of the second story, where he compares the Punies that are following the team to Olimar's Pikmin.note If you check the previously linked page, you'll see that that actually is a shout out to Pikmin in the original game.
"Sheesh Mario, pull out an Ike quote on us why don't you?"
Bowser has an obsession with the phrase "over 9000".
Port-Ed: Nazz claims that her cousin worked part-time at Aperture Science and supposedly was also a test subject of the ASHPD. Despite what one review guessed, it's not Chell. (The author was glad the betareader of the story kept this shout out.)
Naruto's cloud jutsu that allows him to create a small cloud upon which he can fly, which he trades to Sarutobi's ape summoning for a blank summoning scroll.
Naruto covered Sasuke in glitter and stole his shirt, making him look like a vampire.
And after Sasuke's Cursed Seal gets a Luna-made seal themed after the phases of the moon, Naruto (jokingly?) tells him that unlocking the full power of the seal requires Sasuke to shout out "Moon Princess Power!"
The story itself is full of shout outs to other works, usually due to Author Appeal. For instance, chapter 16 starts with Edna and May watching a One Piece movie and chapter 21 starts with the four Eds watching WWE Summerslam.
In the first story, the three main characters sneak into beseiged Central City using a hot air balloon, which is a Call Back of sorts to the 2003 anime adaptation.
Edward Elric's son is named Lucas, after Luke Triton from the Professor Layton games.
The Brotherhood anime showed a photograph of Roy Mustang after the end of the series in which he has a mustache, for reasons unexplained. Many members of the fandom prefer to believe that, as the picture in question belonged to Ed, he had drawn the mustache onto it; this Epileptic Tree is firmly planted in the fanfic.
Arabella and Zsenya's epic fanfiction After the End contains a significant Shout-Out to an in-fandom joke: in the Shipping wars, the Good Ship Harry/Hermione had the iconic symbol of pumpkin pie. In After the End, (a fic that is very Ron/Hermione, based on a website that is strongly geared towards the same) Ron angrily tells his mother that he hates pumpkin pie.
The Three Musketeers (all four of them) show up in paintings to give Ron love advice, and continue to pursue the now-vampiric Milady.
In The Lie Ive Lived, a throwaway line has Harry saying, "Yeah, just call me 'Ambassador Potter', expert at foreign diplomacy and purveyor of international goodwill." This refers to one of author's other works Bungle in the Jungle.
Snape: POTTER! Enough about your mythological creatures and your obscure Muggle literature!
In Weres Harry? when the new Marauders are tasked with organizing the now "Tri-Tri-Wizard Tournament," they pattern the new tasks after the trials the Dread Pirate Roberts overcomes in The Princess Bride.
During an argument with Rarity, Applejack comments that "Ah ain't got no accent!" In fact, the entire subplot going on there appears to be based on that fic.
Checker Monarch appears to be based on Azula, a perfectionist Manipulative BitchChessmaster who is jealous of a younger sibling whom she bullies and has an overbearing father. Moreover, both characters are deeply insecure beneath all their arrogance.
The three main characters of The Golden Armor make a brief appearance in a restaurant setting, and later end up saving Applejack from making a bad situation worse where one of the trio is thanked by name.
Hands: All the time, though no one ever gets Andrew's references.
The two people onboard the Enterprise whose iPhone Andrew and Twilight discover are named after the main characters from Dead Space.
Inner Demons: Queen!Twilight's mind control spell is very similar to a Geass. In fact, her statement when shutting down Cadence's magic — "Never use magic again!" — is very similar to Lelouch's "Never speak again!" moment with Mao. Lezard even refers to this ability as "the Power of the Queen", and his explanation of how it works sounds very similar to the mechanics of Lelouch's Geass.
Though unintentional, Twilight's demeanor throughout this series is nearly identical to her "Mentally Advanced" persona, especially in the cynicism department. The only thing that really distinguishes the two parodies in tone is that Mentally Advanced Twilight would be too terrified of Celestia to back-talk her like Disgruntled Twilight does.
"If Trixie ever comes back, I'm gonna get her in bed with me, just to show her that I'm better than her physically, mentally, and sexually. Three points, you dirty whore."
To Mario Kart: "I heard if you paint it red it'll home in on the closest pony, and if you paint it blue and put spikes on it, it'll automatically home in on the pony that is succeeding the most in life."
The author apparently loves Animaniacs, as Cadence's chapter featured 'mini mares' who find Princess Scootaloo, three of whom are named Yakko, Wakko and Dot. Later, in Discord's chapter, the chaos god opens with his version of The Muppet Show theme.
According to Snips and Snails, Scootaloo is a vampire slayer, with Twilight as her Watcher, the rest of the CMC as her team, and Angel Bunny as her vampire lover. Spike, who is the audience while Twilight is getting much-needed reprieve from the madness, is less than enthused to be cast as the villain.
Rarity: Discord, the Spirit of Disharmony? Good evening, my name is Rarity Bell. As a member of the country and world of Equestria, I ask you to cease any and all supernatural activity and return forthwith to your place of origin, or to the next convenient parallel dimension.
When Rarity mentions how Nightmare Moon was banished to the moon, Jackie wants he to clarify whether she was imprisoned IN the moon, or having adventures on the surface in the form of an adorable filly.
One of Fluttershy's Omega Flight classmates is named Dorothy Gale, who ends up carried off by a tornado to a faraway land.
The beginning of chapter 4 appears to be a reference to The Hangover. Quill wakes up with no memory of what happened the night before, wonders where Filter is, and proceeds to find him on the roof of Sugarcube Corner.
Dual Image might as well be renamed "The Doctor WhoShout-Out Chapter". Not only do Quill and Filter quote the Doctor various times, the scene where Filter, powered up by King Sombra, completely overpowers Trixie and forces her to surrender before forgiving her is taken straight from "Last of the Time Lords".
Rainbow Dash mentions the "Swayback Mountains" at one point. This is a nod to a previous Applejack/Rarity fan fic Butterscotch Sundae wrote.
Chapter 11 opens up with what can only be described as a Take That parody of Cupcakes, and later, Rocket To Insanity. Made awesome by the fact that it's Nightmare's Mind Rape...which Pinkie subverts by lucid dreaming.
Pages Of Harmony: During Rainbow Dash's Mind Rape torture, the story slightly mentions both Rainbow Factory and Cupcakes, two other well-known gorefics. While Cupcakes is only slightly alluded to with Pinkie in one of Rainbow's Mind Rape visions threatening to hack her wings off, the Rainbow Factory mention is quite blatant... and it makes everything much worse.
In a non-MLP example, Pinkie's gesture language and Rainbow Dash's interpretation of it is an reference to Haroun and the Sea of Stories, when Mudra the Shadow Warrior communicates to the Storyteller Rashid in this manner.
Rarity's morning activities in Chapter 7 include a reference to Lyra's endeavors in Background Pony.
"Rarity worked all throughout the morning, only stopping briefly to enchant a soundstone for a mint-green unicorn wearing a gray hoodie. After finishing that, she continued to work on the necklace."
Celestia's response to whether she'd taught Twilight any offensive magic in Chapter 17 is a nod to The Immortal Game. Also a bit of a Take That to the plot.
““If she does, she didn’t learn it from me.” Celestia adjusted one last feather and looked up at Luna. “We covered a few theories on why certain spells have been declared forbidden, but it’s not like I was prepping her for war. The next thing I’m going to hear you say is that I was secretly turning her into a brilliant military strategist so that she’d rise up and become the ultimate weapon.”
Luna rolled her eyes. “Now that’s just absurd.”
"Rarity" asks Grovi about an artifact from The Flight Of The Alicorn while they're walking into Canterlot Castle in Chapter 21, and an airship by the name of 'Fancy Free' is seen from a distance in Chapter 27.
"Is it true that Princess Celestia keeps the Heavenstone from the Pre-Discordian Era in the Royal Vaults?"
Blair responds to Piro's needling about Libra's actions in Chapter 25 with a line similar to one uttered by Gordon in The Dark Knight Rises:
"Celestia forbid you actually have to make a hard decision by yourself, Piro. Be grateful you've somepony to plunge their hooves into the filth for you."
In "Luna vs Ponyville, Part 1: Television", where the first show that Luna watches on Pinkie's television is a pony version of Mister Rogers' Neighborhood, and after changing the channel and trying to find it, she apparently stumbles across a horror movie known as Cupcakes.
In "Luna vs Ponyville, Part 2", Luna finds a copy of the pony equivalent of Twilight, which is apparently a good deal... racier.
Apparently, Priness Celestia mothered a whole group of famous horses, as she explains to Luna in "Luna Versus the Facts of Life." Where to begin? Let's see, Starchild, Shadowfax, Arion, Hengroen, Epona, Widow Maker...
"Luna vs Ponyville 9" gets a massive one for Warhammer 40,000... by Pinkie Pie's parents, who bust out heavy weapons and shout about exterminating "xenos" in the name of God-Queen Celestia when they think their farm house is under attack by dragons. Apparently, it runs in the family.
"Luna vs. Vigilantism" opens with Luna reading a Batpony comic (which appears to be inspired by The Killing Joke). Later Luna (as Mare-Do-Well) performs a dead ringer for the entrance of Darkwing Duck.
When drunk, Trixie starts to quote Londo Mollari from Babylon 5
Trixie's and Twilight's favorite novel is Don Rocinante of Equestria, an obvious shout-out to Don Quixote.
In Longest Night, Longest Day, to keep herself amused, Trixie sings a few lines of "I, Don Quixote," slightly modified to fit into Equestria (i.e., "I am Don Rocinante" rather than "I am I, Don Quixote").
When Lyra says that Pinkie Pie is going to throw Trixie a party, Trixie's response is "Why are you saying that like it's synonymous with 'she's going to drag me into a basement and torture me'?", a reference to Cupcakes.
Scootaloo's introduction to her auntie involves her walking across the ceiling with suction cups, ala a certain Ask A Pony blog.
"She seems to be more caffeine than mare now. Twisted and jittering."
Celestia also mentions that Luna once got her face covered with alfalfa sauce.
Word of God hasn't confirmed this one yet, but the fact that Luna has a magma-powered forge and warns Scootaloo against exploring the castle cellars on her own has led SpaceBattles to conclude that she set the Hidden Fun Stuff loose in her big sister's basement. Whether or not Canterlot also has a Fuck The World lever is also unknown as yet.
The oldshopkeeper introduced in the second half of Celestia vs. Knitting is known simply by his nickname 'Uncle', has a collection of animal talismans, and Dope Slaps ponies to keep them in line.
In Clash of the Elements there is one to Super Mario Bros. Z in Chapter 45 of Part 1 More specifically, the act of having the Star Spirits appear and using their energy to power-up Mario and the other heroes, a concept which, while it didn't get to appear in the actual series, at least got shown in the intro. Thankfully, the author gives Alvin-Earthworm full credit for the idea instead of claiming it as his own.
In Ringshadow's Slice of LifeStar Fox fanfic Butterfly Photographs, Slippy programmed an AI into his pickup truck which has the ability to drive it. Its avatar is a face on a video screen, and its name is Max. At one point a character asks if Max is in one of the stages of rampancy in reaction to Max's slightly odd behaviour.
Decks Fall Everyone Dies. Examples: "Reverse card open" is a shout-out to the MAD videos that feature Kaiba repeating that line. Yami's line calling dice "rolling bones" (astragali) is a shout-out to the manga.
In Mary Mary? Quite Contrary!, there are many shout outs made in the "Sparkly Shiny Alchemist" story. For one thing, the protagonist's full name is Christiana Sophia Maysalee Thomasnote Maysalee is the name of Madge's aunt, for those who don't know. And there's this quote from her "bro" Jeff:
W.I.T.C.H. Fanfic Kieva Lynn's Season Three features C'thulu in one episode. The episode title "The Telemarketing Call of C'thulu" is a play on the title of Real Ghostbusters episode "The Collect Call of C'thulu." They even beat him in much the same way.