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Exactly how many panels do you want this to go on for? Over 9000? Nobody wants that. Nobody even wants to hear the phrase "over 9000."
One of Jane's features in her Crockerdark form is an eye color scheme that bears resemblance to that of Super Buu and Kid Buu. She even imitates Super Buu's hand taunts and fighting style from the battle with Gohan.
Dave jokes about training in a (non-existent) "hyper gravity chamber" on the meteor.
At the end of "[S] Equius: Seek the highb100d", Gamzee demands that Equius kneels, then promptly shoots an arrow. One couldn't help but remember the scene in Black Lagoon where Balalaika pretty much does the same to a psycho-child.
Balalaika:I SAID KNEEL![note that this line is also delivered in English in the VO]
TT: Oceans will rise. Cities will fall. Volcanoes will erupt.
John's admiration for Matthew Mcconaughey displayed in these posters is called back when one of the potential outcomes of the roll of the final die in the Pop-a-Matic Vrillyhoo Hammer against Bec Noir is "MCCONAUGHEY".
The Past and Future trails in the Midnight Crew intermission are a reference to Donnie's visions.
In Jade's introduction sequence, when testing out her Pictionary Modus for her Eclectic Bass, she accidentally creates a ghost image of Johnny 5. Later, during her Alchemize-o-rama, she creates a Johnnytop from her lunchtop and the image, and also attempts to make a massive weapon from a Transformer ghost image, a powerful gun and her own personal Iron Lass suit. She makes...Johnny 5.
Jade finally gets the death she had coming...with SBAHJ captioning to make sure you know how blatant this reference is.
A more subtle and less funny example is when Aranea manipulates Doc Scratch's clock to make Jade's death "Just". The clock makes a loud "DING DONG" afterward.
"Ding dong the witch is dead..."
After dying, Jade somehow appears in Calliope's bubble and turns the spiral path from white to the hue of the yellow brick road. Her reaction?
CALLIOPE: PAY NO ATTENTION TO THE GIRL BEHIND THE CURTAIN!!!
Terezi asks John to think of a phrase he can remember for something she wants to try. John comes up with it while looking at Terezi's ruby slippers, which she took from a witch who got crushed under a house:
And Sopor Slime fits neatly into the likes of Slab, Scrape, Slice and Slunkie, being a psychoactive troll drug that starts with 'S'
When Colonol Sassacre is killed, it says "People would think reports of the man's death were greatly exaggerated. But they weren't." This is based on a famous Mark Twain quote, whom Sassacre is very loosely modeled after.
Not only does Cronus' backstory reveal that he's a failed Harry Potter imitation (with magical scars, no less) who eventually rejects magic altogether, but presumably, Lord English is his version of Voldemort, and the Jujus are his horcruxes. And the only known "Juju breaker," Crowbar's crowbar, shares a color with the Sword of Gryffindor's house of origin.
Vriska and Tavros's tumultuous relationship involves frequent references to Peter Pan, with Tavros as Peter and Vriska using tropes from both Tinkerbell and Hook. The shoutouts cover the entire expanded universe, including the filmed theatre adaptation and Hook, but also use references that only appear in the book, such as Vriska's weapon being a collection of eight stone dice called the Fluorite Octet (a pun on Captain Hook's last words, "floreat etona").
As of the end of the Midnight Crew intermission, Vriska, Spades Slick, the harlequin doll all bear the same set of injuries: An injured eye and a missing arm. These are the same as the injuries borne by Hook.
While Mituna's introduction in Openbound included at least one misspelling of the word "helmet" as "H4ML37", it is only in [S] [A6I3] Ministrife!!! that Kurloz plays on the reference by showing up to the Meenah-Vriska battle/costume party dressed as a prince at the same time Mituna shows up asking for his helmet.
The resemblance of Crockerdark Jane's costume design to that of Little Red Riding Hood would be coincidental due to the Crocker colors...were it not for the fact that the one that makes her transform is Grimbark Jade, who has been turned by the Condesce into Jane Riding Hood's Big, Bad, Badass Wolf.
Not to mention that both have alternate incarnations that were surrogate grandmothers...
One of Kurloz' gifs in his signing conversation with Meulin is the famous "Tenth Doctor in the rain" clip from the end of "Journey's End". Given Kurloz' service to an entirely different kind of Lord of Time, Meulin could be considered a companion.
A mention for Caliborn's suspiciously similar sounding godtier "Lord of Time". Also just like his adult self and the Eleventh Doctor, Caliborn rocks a bowtie and suspenders.
The stripes on Lord English's Cairo Overcoat resemble a flashy version of the Fourth Doctor's scarf.
In recent strips, Roxy discovers a magical crack in her bedroom.
When Lil' Cal is given to Alpha Jack Noir and Jack stares into Cal's eyes, Caliborn's soul takes him over completely when he sees Cal's eyes become Lord English pool balls. The subsequent events suggest that like anything that sees or records a Weeping Angel's eyes, that which holds the image of Lord English becomes itself Lord English.
Later, John's costume resembles Link's outfit in Wind Waker and he comments on it.
Meenah finds one of the empty bottles Rose has been using for alchemy... and promptly throws it away, because it's just an empty bottle. note In The Legend of Zelda, bottles are rare and valuable items.
In addition, one of the songs on the "Dave, Rose: Shut Up And Jam" (which is itself a reference) is called "Octoroon Rangoon". In Barkley, Shut Up And Jam: Gaiden, one of the party members is Balthios, who is referred to as "the octoroon note or 1/8 black great-grandson of LeBron James".
Gamzee's constantly dances, similar to shop keepers in the Secret of Mana.
Not to mention he's jokingly acting like an innkeeper and charging people to rest in his pile of horns.
Entering Trickster Mode plays (most) of Totaka's Song.
The Sims (with the house-building and item-placing) and Spore (with all the Space Compression planetary hijinks) are also cited inspirations. Particularly in naming "Sburb", by Word of God a "deliberately ugly word reminiscent of the name of a Sim game".
The shop from Final Fantasy VI makes a cameo appearance in AlterniaBound's Trickster Mode screen, and ends up in the story itself later on, as part of Gamzee's trap for Terezi at the end of Year 2/Disc 1.
The flashes at the start of Act 6 Act 3 are a shout out to Myst, according to Hussie.
Lara Croft, for obvious reasons, influenced Jake's LOMAX outfit in Act 6 Act 4.
Though Lord English's name was at first unintentionally similar to that of Lord British from Ultima, it seems that his servant Gamzee, given the discovery in A6I4 that he's nigh immortal in all timelines, is rapidly becoming an Expy of Chuckles, Lord British's jester.
And it's used as a Mundane Utility by Dave to make coffee. And there's this piece of dialog:
DAVE: two hot revitalizing cups of shitty coffee
Word of God instance: Hussie has stated that, of her extensive gaming repertoire, Roxy's favorites are EarthBound and Pikmin, two titles he himself particularly enjoyed.
The interactive games, starting with AlterniaBound are meant to resemble... you guessed it.
The song "Plumbthroat Gives Chase" from the "Squiddles!" album begins with Skipper Plumbthroat saying "This might not fit my... rude outer ego, but I really love drinking tea and eating broccoli," which is a reference to a line one of The Sharks says in Onett's arcade. "To tell you the truth, I like drinking tea and eating fresh vegetables, but that doesn't fit my super cool image."
A dinosaur from the Dinosaur Comics website's background appears momentarily here. Ryan North thinks it signifies something more.* "Believe you me: this is no mere shout-out to good, sensible web design elements. I believe this to be an acknowledgement of what Andrew and I have long known in our individual and respective heart of hearts: that Dinosaur Comics and MS Paint Adventures take place in the same universe, that one will segue into the other after only a few million years have passed, and that just as Steve Urkel and Carl Winslow could in theory go for a walk and bump into Balki and cousin Larry, so too will this pterosaur from my site one day happen to fly over the events which set up the adventures now being chronicled on his site, these adventures that take us through time and space, these adventures that have let us take control of the bodies of at least three children so far, these - these MS Paint Adventures."
One of the possible outcomes for John's roll of the final die in the Pop-a-Matic Vrillyhoo Hammer against Bec Noir is "T-REX".
invoked The end of Act 6 animation's URL ends in the letters "DOTA" which presumably stand for Death of the Author, since, well, Hussie has just been killed by Lord English. Death of the Author is also a famous 1967 essay by Roland Barthe. In it, Barthe suggests that the author has no authority over the text, the true meaning of which is created uniquely in each reader's mind according to their own impressions as opposed to the intentions of the author. Kinda appropriate considering MSPA's reliance on audience participation, fixation on cultural references and exploring the boundaries of fiction and reality. And of course, Hussie's self-inserted character's inability to control events at this point in the story.
In the same intermission, we have "Dave's "ebubbles", which spout out seemingly random sentence fragments from Dave's previous pesterlogs. Both the name and the result are reminiscent of the infamous spam Twitter account Horse_ebooks.
The entire flash segment with Meenah is very much an extended parody of Tumblr and the kinds of people who frequent it.
Said parody is taken Up to Eleven with Meulin. In addition, Mituna is a parody of Imageboards, 4chan in particular.
Dirk's gas mask in the Act 6 Act 4 flash bears similarity in both design and color to the mask of Tahu from BIONICLE.
A few Rainbow Dash pictures can be seen in Dirk Strider's room. While he purports to have a "strictly academic" interest in cartoon ponies, he soon admits that his affection for Rainbow Dash, at least, is totally unironic.
One of Meulin's gifs from her signing features Apple Bloom pressing an "Unsee" button.
In the Tricksterlog accompanying Dirk's "Engage" flash, Jake drunkenly misspells "everybody." No, the result is not "EVERYPONY," as you might expect; it's "EVERYBRONY."