This episode opens with "The Road So Far" - a series of clips accompanied by "Kansas" song "Carry On Wayward Son", showing what has happened in the season to date. This recap method is later used in every season finale of the series.
In this episode, when John is talking to Meg on the phone, she demands he meet him at a warehouse to give her the colt. She says the warehouse is in Lincoln, Nebraska on the corner of Wabash and Lake. Which is clearly a reference to The Matrix.