We find that Flam Flim-Flam has dyed his mane and mustache black and changed his name to Professor Destiny, a nod to Professor Fate from The Great Race. His sidekick Otto Bomb is pretty much a pony version of Professor Fate's flunky Max.
Pip's compliment to Apple Bloom on her opera dress is a reference to Thomas Dolby's "She Blinded Me With Science".
And not too long before, in Chapter 28, Rarity raises surprise that Fancy Pants isn't getting in on the betting action. His response? "Why my dear Rarity, I'm shocked... shocked that you would insinuate such a thing."
Also at the end of chapter 29, when Chrysalis is offered a drink, she declines, since "Alcohol makes me spew caustic foam from my splanch." This bizarre alien organ was invented by the webcomic Darths & Droids, where it is eventually established as an additional organ possessed by shapeshifters.
Applejack and Soarin' get engaged in the middle of a fight, ala At World's End.
Strongheart has to convince one of her fellow buffalo that Flies Like Thunder isn't really a legendary buffalo messiah: "He's not the White Buffalo, he's a very naughty boy!"
Flies Like Thunder and his companion Long Range are obviously based on The Lone Ranger and his Native American companion Tonto, with the roles reversed.
In Chapter 33, Destiny and Insanity accidentally set the Appleloosan jail-house on fire, and Austrian-accented Negasi Fleidermaus is tasked with escorting some of the prisoners out through the smoke. He tells his charges "Come vith me if you vant to liff."
Also in Chapter 33, Sheriff Silver Star's deputies are Trigger and Nutmeg, AKA Nutsy. Nutsy and Trigger were two of the vulture mooks from Disney's Robin Hood.