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Voldemort's speech before killing Harry is from the finale of Avatar: The Last Airbender.
Ginny tells Harry, "We kissed at the Yule Ball, and, well, I thought we were going to be together forever . . . but we're not." This is almost identical to what Aang says to Katara in The Ember Island Players (though he refers to the invasion of the Fire Nation).
The scene when Ron and Hermione first kiss is the scene between Aang and Katara before the fire nation invasion where Aang kisses Katara. The dialogue leading up to the kiss is almost identical.
The sting from Seinfeld plays every time Ron enters a room. This continues in the sequel.
Dumbledore's and Hermione's dialogue about what would happen if Harry didn't enter the tournament is from Ghostbusters.
Harry compares his relationship with Ginny with that of Spider-Man and Mary-Jane.
Voldemort quotes Jafar with "How many times do I have to kill you, boy?"
Snape's death scene is similar to Yoda's, complete with "There is another Horcrux."
When Harry and Ginny dance at the Yule Ball, Harry says, "Ginny... Ginny I'm feeling kind of dizzy." Ginny replies with, "Well, maybe we should stop spinning." Harry then responds with, "We have stopped spinning..." This comes straight from the scene in Anastasia where Anya and Dimitri are dancing.
Per usual, there is an extended Spider-Man analogy.
When Seamus is telling a scary story in Hogsmeade, he's telling everyone about a scene from IT.
Who knows if this one is intentional, though it certainly seems that way: the Death Eaters' bridge in "It's Not Over Yet" sounds (and staging-wise, looks) very similar to "Ewigkeit" from Tanz Der Vampire.
A reference to the Team's past show Starship appears when one of the mob bosses tells his henchman that, "You make me laugh like nobody else," a direct quote of something Buggette said to Bug in the former show.
When Robin asks Candy if she is hurt after getting hit by Sweet Tooth, she replies that "it felt like a kiss," which is an allusion to a song by The Crystals. It's also something said by Harlequin about the Joker's abuse of her in the comic 'Mad Love'.
"Robin make Batman happy," is a reference to the line "Ursula make George happy" from George of the Jungle.
Forget Sherlock, the original stories were full of Ho Yay.
Evil!Sherlock: Now I'll never be able to walk Evil!Watson down the aisle!
The "rabble rabble" gag the citizens do may be a SO to a minor recurring gag in the earlier seasons of South Park.
"I say we KILL the Bat!" All of the emphasis and the pattern the words are delivered are a clear shout out to Gaston's "I say we KILL the Beast!"
Frequent mentions of the heroes wanting to play Nintendo with each other.
There are many shout outs to The Dark Knight Saga including, "I won't kill you, that doesn't mean I have to save you", "This town has shown you that's full of people ready to beleive in good" and Alfred saying the Batcave was used to help runaway slaves. Also one of the Gotham citizens has a "I believe in Harvey Dent" shirt. Another has a "Why So Serious?" shirt
Voldemort says that the diary works on the same rules as Death Note.
This is also an example of Throw it In. In the script, Voldemort hid behind a desk. There were no desks on stage, so Voldemort's actor, Joe Walker, improvised a line about how the diary worked. Later, Harry (Darren Criss) brought it back up and Joe played along.
Aladdin quotes Light Yagami: "Could anyone else have come this far?"
Aladdin's split personality is very similar to a scene from the first Spider-Man film.
Obviously, as this is essentially a show consisting of new arrangements of Starkid's greatest hits, it's chock-full of shout outs to their previous works. However, there are also some new ones in there, such as the Funny Background Event where Brian Holden, launching into "It's Not Over Yet" from A Very Potter Sequel in response to Joe Walker doubting his plans, force-chokes Joe for not believing in him.