The playhouse Regina is building is based on her castle as the Evil Queen.
When David is on the toll bridge waiting for Mary Margaret, someone drew a pink R onto the TOLL BRIDGE sign making it TROLL BRIDGE.
The genies line, "In my time I have granted a thousand and one wishes and I have seen them end poorly a thousand and one times..." is a reference to One Thousand and One Nights.
As Regina tells Emma and Sidney, the present events in Storybrooke take place three weeks after Desperate Souls (2012).
According to the slide projector, Storybrooke's coat of arms is an apple tree with a beehive in front of it. The tree is a reference to Regina's apple tree and her fruit of choice, while the beehive is a subtle nod to her status as the Evil Queen: A bee colony consists of workers, drones and a single queen. In addition, beehives are often placed in apple orchards and other orchards because honey bees ensure cross-pollination and are therefore crucial to running a fruit orchard.