At the beginning of the episode Sam and Dean play Rock Paper Scissors to see who will have to talk to Bobby. This is interesting because Dean always throws scissors losing to Sam. In this scene he throws scissors and beats Sam for the first time in the series.
The episode features many Final Destination references, whether intentional or unintentional. The plots both follow a group of people dying after escaping fate, and both even feature a character being run down by a bus right in front of the main characters as they stand by and watch in horror.
Sam tells Balthazar, "You totally butterfly-effected history." He is referring to the chaos theory principle, that a small change in the initial condition of a system will result in larger changes in later conditions.
At the Travel Agency, there are posters on the wall for Detroit as "America's Top City" and one for Cuba. Since Detroit has been in decline for decades now and Cuba at that time was still under a trade embargo that barred tourist travel, this reflects differences in the new timeline. The fact that Ellen and Jo didn't die in Detroit suggests that those events played out differently, which according to Castiel, Sam and Dean should still remember.
In the alternate timeline there is a photo of Bobby and Ellen outside of Bobby's place by a sign that reads B & E Repair Shop ( as in Bobby and Ellen) instead of the usual Singer Auto, which we see when the boys return the original timeline.