There is a Persona 3 calender on the wall in the main character's bedroom.
The story that Adachi reads to Nanako about a lonely pink alligator is a reference to the story Akinari Kamiki from Persona 3 writes about.
During the month of January, when you go to the garden to harvest bugs, Teddie will often say, "Hold on there, Sensei! It's dangerous to go alone! Take me!" This is a reference to the old man in the first Legend of Zelda game, who said, "It's Dangerous to go Alone! Take this!"
During the beginning of Marie's Social Link, she asks the protagonist what the word 'Steak' is short for. If you choose the option, "It's short for Beefsteak", she will reply that it should really be shortened to Fsteak. This is likely a nod to Hiimdaisy's Persona 4 fan-comic. In the comic, Chie is asked for another word that starts with a "F", to which she replies with "F-steak?"
Both Chie and Teddie's voice actors (Tracey Rooney and Dave Wittenberg respectively) were unable to reprise their roles. They were replaced with the "Persona 4: The Animation" actors, Erin Fitzgerald and Sam Riegel.
In the cutscene for the Ski Trip, if you look a Rise's jacket, you'll see "Lovers '06". This is a reference to Rise's Arcana, "The Lovers", which is the 6th Arcana (VI).