The title of "Wild Movie" references another one of the author's Calvin fics - "Wild Movie Collection", in which the duo act out various action movie scenes. Calvin himself mentions it in-story as well.
A good amount of the Original Characters are from the author's earlier fics, which may cause some confusion for new readers.
In chapter 10 of Port-Ed, as the Eds are about to incinerate the Curiosity Core, Ed states that it will be just like Narbacular Drop. Narbacular Drop was the student project that eventually became Portal.
Shinnok's understanding of the universes he handles leaves us with plenty of these in the New Look Series, such as Sonic's hydrophobia, or Ash's memories of the Ashley incident.
The Naruto/TMNT crossover Teenage Jinchuriki Shinobi has Raphael in a tag team with Hyuuga Neji against Kidomaru, a sound ninja who has spider-like properties. In the 2012 series of TMNT, Spiderbytez was a result of Raph's anger problems.
Hisa vaguely references Yasuko losing to someone younger than her in the past, a reference to Yasuko's defeat against Koromo.
Toki, while hospitalized during the match between Pravda and Black Forest, wishes that she could use astral projection to help Ryuuka know where to go in order to win, much like Ryuuka's ability in the captain match of the semi-finals of Saki.
As the Saunders team discusses how to deal with Oarai, Mairu suggests that they could afford to make some sacrifices to gain the advantage, not unlike how she favored giving up the vanguard match by placing someone who wasn't good enough to win but wouldn't go under 0, and having the stronger players recoup the losses. Kirame, the said sacrifice from canon, suggests that it would be a way for them to help the team, but Himeko, who, in canon, had reservations about the plan, tells Kirame not to sell herself short.
In Toki's final scene, it's pointed out that she can't see the future, a reference to her ability in Saki.
In Fist Of The Moon, Ranma shows off her Gender BenderMode Lock to try to quell a hostile girl's gym class she's been assigned to, protesting that she is just as much a girl as they are. Akane ends up adding her two cents by saying, "and better built to boot", something Ranma used to insult her with in the first volume of the manga.
In the fanfiction series, Negaverse Chronicles, events in theNegaverse are shown rather than those of the regular universe from the show. In Bushroot's backstory, Dr. Gary and Dr. Larson start jokingly teasing him about how the potato Bushroot has been experimenting on is his new girlfriend, that it might start sucking his blood like a vampire, and that russets are evil. All of these things refer to an episode of the show, "Night of the Living Spud," where the normal universe's Bushroot tried to create a mutant potato girlfriend for companionship.
The other is to do with Clan Tourneys. The Clan Tourneys shown are one-on-one duels, unlike the six-on-six shown in the games. It is mentioned that the Clan Tourneys used to be like the games but starting with the one we're shown, a format change was made to give smaller clans a chance against the larger ones.
In Power Games Alicia mentions a story about a princess who slept for centuries after her kingdom was destroyed, which is referencing Ixpelliaand serves as Foreshadowing for her early appearance in in the story.
In The Service makes a huge number of them. A Material-S reference dies at the hands of Vita in the second chapter; Isis Eaglet is a Combat Cyborg based on early fan speculations from her resemblance to Subaru and Ginga Nakajima; Uno and Signum discuss a world called "Lamia" and Uno describes it as "the loveless place" referencing Signum's status as an expy of Lamia Loveless; people who encounter Cypha of Huckebein tend to compare her to Signum though the two never meet in this continuity, referencing their fight in the canon.
The fanfic, Equestria: A History Revealed, is practically built upon the whole concept, with references from large past events to the minute historical details brought up in the show. The author even slips in some references to past generations and fanon material. The Bibliography itself should be prominently mentioned in this, with tiny jokes and details regarding background characters and historical books brought up once in the show.
Anthropology: Lyra's birth name was Heartstrings, but she prefered the name Lyra, since it was more of a human name. A reference to the fact that when her toy first came out, it was named Heartstrings, but the fans prefered the name Lyra, and thus she renamed as such.
In Kitsune no Ken: Fist of the Fox, the code-names that the Kyuushingai use to identify each other are references to the Bijuu each of them hold in the main series—more specifically, the Biijus' actual names. For example, Naruto is known as "Kurama the Fox"; in the main series, Kurama is the name of the Kyuubi, whose form is that of a fox. Naruto lists off all the names in Chapter 3 to prove he is a former member of the Kyuushingai.
Empath: The Luckiest Smurf : Narrator in "Empath's Wedding" recites a modified version of his Gargamel battle sequence speech from The Smurfs during a similar one in the Imaginarium, with Grouchy reacting the same way.
Narrator: There comes a time when every Smurf must stand up for what is good and cute and blue in the world. And on this very night before Empath and Smurfette's wedding, that time is now!
Grouchy: Hey, seriously?
Narrator: Sorry, it's kind of what I do.
In "Gargamel's First Catch", which is an adaptation of "The Smurfnapper" from the comic books, Duncan tells the fallen Gargamel that he would have made haggis from his innards, which is what Gutsy said to Patrick Winslow in The Smurfs movie.
Jokey in "Empath The Bandit Smurf" (an adaptation of "The Jewel Smurfer") lampshades that he should have been the one who was lost and taken instead of Empath, since that's what happened in the original story.
In the original Spider-Man comics, Peter Parker would sometimes sarcastically observe that "the old Parker luck is running true to form" whenever his Butt Monkey status came back to bite him. In Ultimate Spider-Woman: Change With The Light, Mary Jane Watson is much more of a Butt Monkey than Peter, and so she makes the same references to "the old Watson luck" when things go badly for her as well.
Reimagined Enterprise: All the time. One example is that, in a flashback showing the Eugenics Wars, Khan Noonien Singh's fanatical supporters shout their leader's name as a war cry...so in other words, "KHAAAAAAAAAN!"
Chapter two of Bait and Switch has a mention of Eleya straightening the hem of her uniform jacket as she gets out of her chair on the bridge, something Patrick Stewart did all the time that got nicknamed "the Picard Maneuver".
Legacy of ch'Rihan borrows Nero's "Hello, Christopher, I'm Nero" line from the 2009 Star Trek movie, only here it's Commander Saeihr t'Ethian he's talking to.
Reality Is Fluid: Given that the first part of the story is set on or near Deep Space 9, commanded by Captain James Kurland, the author couldn't help throwing in a "Kurland here" in one conversation.* A meme internal to Star Trek Online, deriving from Kurland's voice acting in the mission "Boldly They Rode".
Shane's reaction to murdering Rick in Better Angels is a lot colder than Rick's reaction to murdering Shane in canon. However, there is a sentence that references the scene where Rick blames Shane for taking things this far, where Shane imagines Rick's corpse shouting this at him.