Bobbi Morse makes a reference to the MKULtra trials. These were experiments carried out illegally by the CIA to figure out ways to control the mind when interrogating someone.
The son of Lou Ferrigno, Lou Ferrigno Jr., plays the HYDRA sleeper agent who released Whitehall from "The Rat." Lou Ferrigno (Sr) is best known as a bodybuilder and the actor who played the Hulk in The Incredible Hulk (1978).
Bobbi mentions that Bakshi has "got that whole classic Bond-Villain thing going on." Simon Kassianides, who plays Bakshi, appeared in the Bond film Quantum of Solace (2008).
Coulson's blue tie was a gift from Audrey, the cellist who was first mentioned in The Avengers (2012) and seen in season one's The Only Light in the Darkness (2014).