In the screenshots released of Aiden's smartphone functions, you can see an icon that resembles the symbol of the Assassin Order, except flipped, connected to Pieces of Eden. Both are from the Assassin's Creed series.
At least one NPC is described as a "former Abstergo employee," a reference to Assassin's Creed.
In any clothing store, you can hack a fish mounted to the wall above the changing rooms to make it sing.
One child you can find in Chicago is playing Ubisoft's RPG Child of Light on a tablet.