Twilight's wondering about if the Little Planet's appearances cause natural disasters is a reference to the Transformers Generation 1 cartoon, particularly the episode "The Ultimate Doom", when Megatron was able to bring Cybertron to Earth (similar to what Sentinel Prime tried to do in "Dark of the Moon").
When Sonic and Twilight are talking, the sequence that takes place is similar to the scene in Sonic the Hedgehog (2006) where Sonic and Elise are in the field.
The log Twilight mentions when the group is running from the giant alligator is meant to be a reference to Dinosaur Jungle from Sonic and the Secret Rings.
When everybody's bowing to Celestia and Luna, Sonic's bow is a reference to the way he bowed to Lady Nimue in Sonic and the Black Knight while Espio's bow is a reference to the way Monkey Khan and Sally bow to the Bride of Constant Vigil in Sonic Universe #16.
Although it's never stated, the place Chrysalis sent Sonic, Shadow, and Gilda to was Quartz Quadrant.
When Twilight is using Sonic and Tails to attack, it's a reference to the Combo Attack from Sonic the Hedgehog 4: Episode II.
Sonic and Rainbow Dash's final attack is based on what Sonic and Knuckles did in the Sonic X episode "Trick Sand".
The device that falls out of Trixie's ear is based off the neuro-controller Eggman put in Sonic's ear in the 2007 Free Comic Day Special, which was probably inspired by the chip that got caught in Sonic's ear in the Sonic X episode "How to Catch a Hedgehog".
Sonic having a cell phone is a reference to the iPhone version of Sonic the Hedgehog 4: Episode I, which had a unique idle animation of Sonic pulling out an iPhone and holding it up to his ear to listen to music.
Tails' explanation of the device controlling Trixie references both the Sonic X episode "How to Catch a Hedgehog" and the 2007 Free Comic Book Day special for the Archie comics.
Sonic's mention of another candy land with cotton candy clouds is a reference to the game "Sugar Rush" from Wreck-It Ralph, which does, in fact, have clouds that are made of cotton candy (different from Discord's, obviously).
The idea of the missiles being filled with candy comes from Sonic Shorts.
One of the names Silver suggests for Twilight's version of the Psychic Knife is Mana Sword, which Tails thinks is already taken. This is a reference to Secret of Mana.
Princess Celestia's interest in the donut after hearing people have been sitting on it is a Molestia reference.
The battle against the Egg Pawn army is inspired by the scene in Turtles Forever where the 1987 Turtles and 2003 Turtles and Splinter are battling 1987 Shredder's Foot Soldiers, Bebop, and Rocksteady in front of the Technodrome.
Sonic wondering where Marine came from is a reference to the raccoon's surprise appearances near the end of Sonic Rush Adventure, seemingly showing up out of nowhere.
When the group attacks Captain Jelly, the Babylon Rogues' Extreme Gear briefly transform into their respective forms in Sonic Riders: Zero Gravity.
Marine's line "You're a princess" is a line said by Sonic in the Sonic Sat AM episode "Dulcy" to Sally.
Tails knowing about Kingdom Valley is a reference to the "Team Attack Amigo" DLC for Sonic the Hedgehog (2006), which has you play through most of the levels from the game and the Egg Genesis boss with Tails, Blaze, and Omega. One of the levels Tails goes through is Kingdom Valley.
Sonic running across the Egg Carrier is a reference to the Sky Chase levels/games from Sonic Adventure. When Sonic wonders if the Egg Wyvern is one of Eggman's scrapped creations, he's referencing the fact that the Sky Chase Act 1 dragon can still appear in the game despite not being finished.
In the battle with the Egg Wyvern, Sonic teases Eggman by saying "How much is it costing you for these things to fire this long? Four hundred thousand rings?" This is a reference to Team Fortress 2, specifically to Meet the Heavy.
The screen that the Time Eater creates is based off the monitors that show how to do the combo moves in Sonic the Hedgehog 4: Episode II and the monitor Eggman uses to reactivate Metal Sonic at the beginning of Episode Metal.
When Sonic and Tails team up to attack the Time Eater, their combined attack is the same attack Sonic and Knuckles do in the Sonic X episode "Map of Mayhem".
Sonic mentioning that Discord using magic to take his speed away is a reference to the Sonic Sat AM episode "Super Sonic", where a wizard DOES take Sonic's speed away with magic until he gets his computer of spells back from Robotnik.
The table that Discord creates to hold Rainbow Dash down is a reference to Cupcakes.
When Discord says brown would work for Sonic when his fur is sticking straight up, it's an allusion to how Sonic looked in Sonic the Comic before he met Dr. Kintobor, got his Power Sneakers, and broke the speed of sound for the first time. That incident fused his quills together and turned him blue; before that, he was really spiky and brown.
Tails' thoughts about a beam creating a copy of Sonic is a reference to Sonic The Fighters, where, when both players are the same character, Eggman shows up at the start and uses a beam/ray that, except for Honey the Cat, creates a completely gray copy of the character.
Some of the things said at the beginning of the chapter, particularly Eggman's rant and Sonic's response, are based off of dialogue from Issues 229 and 200 from the Archie comics.
Applejack's "Apple Sphere" attack is based off of both the move Aura Sphere from the Pokémon series and the Hadoken attack from the Street Fighter games.
Eggman's reference to using the Elements of Harmony as part of a wrestling costume and the name Discord gives him refer to the Sonic X comics, where Eggman did briefly become a wrestler named El Gran Gordo.
When Super Sonic passes through Discord, it's technically a reference to Super Sonic's first appearance in the Archie comics, but it also refers to the 360/PS3 version of Sonic Unleashed, where Super Sonic is shown being able to pass through one of Perfect Dark Gaia's hands when he moves in to deliver the final blow.
The appearance of the Dark Forces is a reference to the Nightmare Moon arc in the main FiM comics. Rarity called them "wooshie things" when they took her captive and were attempting to break her.
The final scene in the White Space makes three references: first to the scene in Sonic the Hedgehog (2006) after Solaris' defeat, when Sonic and Elise see Solaris' true form before being sent back in time, the end of The Subspace Emissary in Super Smash Bros. Brawl, when all of the areas that were taken by the Subspace Bombs are returned to normal following Tabuu's defeat, and the ending of "Genesis" in the Archie comics, when Sonic and Sally are reaching out to each other as the world fades to white.
The opening sequence with Rainbow Dash waking up to whiteness is a reference to the aftermath of "Genesis" in the Archie comics, when Sonic is just waking up after causing Chaos Control and is briefly remembering the alternate Mobius.
Orbot's mention of Eggman taking a night off every week to go somewhere is a reference to Eggman being a part of Bad-Anon in Wreck-It Ralph. Sonic mentioning going to a party sometime is a reference to one of his cameos in the same movie.
Some of the things Spike says when he's playing with the Sonic and Amy figurines comes from the Sonic X episode "Cruise Blues". Some of Sonic's dialogue during the talks with Twilight and Pinkie comes from the episode "Friends 'til the End".
The talk about Sonic having a band is obviously a reference to Sonic Underground, but Sonic's mention of Vector being a part of a band with him is a reference to the scrapped Sound Test from the original Sonic the Hedgehog, which was supposed to feature Sonic and Vector together with several other band members playing the songs.
Omochao appearing with a camera to take a picture of everyone is a reference to the normal ending of Sonic Advance 3, where Omochao appears with a camera to take a picture of Sonic, Tails, Knuckles, Amy, Cream, and Cheese.
Adventures on the Friendship Express: Chapter 1
After Tails explains what the gang is going to do with the portal in their way, Pinkie says “Now you’re thinking with portals, Tails!”. This is GLaDOS's final line in the trailer for the original Portal.