During "Apples to the Core", Pinkie's line "You're more fun than the color pink" refers to the G3 special "Positively Pink", which began with Pinkie painting the town pink and singing about how much she loves that color.
Friendship Report: The Apple Family learned family loves each other and forgives each other for their mistakes, while Pinkie learned even close friends can be part of a family as well.
Roughly around the 17-minute mark, right when Pinkie plows into Applejack and the camera pans to follow them, a faceless pony can be briefly seen through the trees on the far right for a split frame, likely bearing a strong resemblance to Slender Man.
While in Goldie Delicious's cabin, one of the doodles on Pinkie's mirror reflection is a pair of wings, referring to the early development where Pinkie was originally envisioned as a pegasus, and that her character is based on the G1 pony Surprise.
First episode where Twilight is only present for the cold open.