Warning: There could be some spoilers.
Top 5 Games to Play About the End of the World
Crystalis - In 1997, Nuclear War happened. In the preceding 100 years mankind has risen from the ashes, forsaken technology and gone back to the ways of magic. What also rises is the evil Dragonian Empire who wish to subjugate the new world and are using magic and technology to accomplish it. As the hero, it is your mission to help the resistance and stop Dragonia's attempt at another Apocalyptic event.
Final Fantasy III/VI - One of the few games that I can remember where your character(s) experience the Apocalypse first hand. This time at the hands of the power mad clown, Kefka. I don't think I need to describe FF3/6's plot past this as it is up to your group to stop Kefka's further ambitions for destruction.
Fallout franchise - While not a franchise I am familiar with, I do know that it involves life after a Nuclear War and dealing with all the mutants and stuff that go with it.
Fragile Dreams: Farewell Ruins of the Moon - As Seto, you search through a post-apocalyptic Japan in search of more people and a mysterious girl you meet early on. As you go you will learn why the people of the world vanished seemingly into thin-air and fight ghost pants. Ghost pants that laugh at you. Stupid ghost pants.
God of War III - This is the only game in this list that differs from the norm. Typically you play as character reacting to events after the Apocalypse but in God of War III Kratos single-handedly brings on the end by brutally murdering most of the Olympians who have wronged him which in turn destroys the balance of whatever aspect of order that God presided over.
Now as I said this is a shortlist of games in a plot idea that is very common in gaming. So enjoy Rapture Day and if it turns out I was wrong, well, I'll see you in hell.