In the game, one of the notes mentions that they "sang a bit about not setting the world on fire". This is a reference to the song "I Don't Want to Set the World on Fire" by The Ink Spots, most likely for it's use on the Fallout 3 soundtrack.
The unlockable character Pancakes is a reference to another game made by Robot Gentlemen Studios called Mr.Pancake, which hasn't yet been released to the public.
If Mary Jane is left behind in the explosion and is let in by the player if she survived the explosion, she will claim that she survived the explosion by hiding in a refrigerator, this is a reference to Indiana Jones And The Kingdom Of The Crystal Skull where indy hides in a refrigerator to survive an explosion.
The Game Mode Difficulties are all named after real life bombs, "Little Boy" is the name of the bomb dropped on Hiroshima in 1945, "Fat Man" is the name of the bomb detonated over Nagasaki in 1945, and the "Tsar bomb" is a hydrogen bomb tested in 1961, in the Novaya Zemlya archipelago at Sukhoy Nos.