When Peter and the Olivia "over there" talk about the difference between universes, Peter looks a famous cover comic starred by Green Lantern and Green Arrow, but in this alternate universe, both have been called Red Lantern and Red Arrow.
In the first part of this two-parter, the alternate Fringe agents nearly used a quarantine device to contain an event. Walter and Bell's journey to Walternate's lab at alternate Harvard showed the effects of such a device, which closely parallel the effects of the weapon used on the bus in episode 1.3.
When Peter is shown his new room by 'Olivia' on the wall are several pictures relating to comics. There is the lightning picture of Frank Miller's The Dark Knight Returns but where Batman should be there is Superman.