When Deke is in the storage area checking out the Twinkies, the long shot shows a group of brown cardboard barrels that are water-stained and distressed. These are authentic Civil Defense barrels that were stored in government fallout shelters starting in the 1950s. The contents varied but could include food, water, medicine, and other things. The version that contained toilet paper also included large thick plastic bags and a black plastic seat.
In the final scene Ruby wears a Stardust Nation t-shirt. "Stardust Nation," by Deborah Levy and illustrated by Andrzej Klimowski, is a graphic novel dealing with themes of personal identity and memory recall/repression, similar to what Werner Von Strucker is experiencing.
When Coulson and Daisy first encounter Lewis Casalino, Daisy lists some of his aliases. Among those are "William Pratt" which is Spike's real name on Joss Whedon's other show Buffy the Vampire Slayer, and "Marion Cobretti" which is Stallone's character from the movie "Cobra".
Coulson tells Mack, "Mack Hammer, can't touch this" about the Gravitonium. It's from M.C. Hammer's song "U Can't Touch This."