In the begining of the episode Maria Hill is talking on the phone and says dealing with Congress is like being in Kindegarten. "Where is this Fridge, and who or what is a Man-Thing".
Man-Thing is a known character in Marvel comic books. (link)
Short version, Man-Thing was a human scientist who was working in a secret lab in Florida trying to replicate the Super Soldier Serum that was used to create Captain America. When the scientist discovers that his wife is a deep undercover spy for AIM (Iron Man 3 fire baddies), he destroys all his research and tries to escape with the last sample of his formula. He ends up injecting himself with the serum hoping to save himself but instead is mutated into the 'Man-Thing'. As Man-Thing, he can spray an acid mist and he ends up scarring his wife's face when she attacks him.
Man-Thing's wife appears in Iron Man 3 (link) and is referenced by name and has the scar.
When Ward is starting up the SHIELD airplane to leave, he is contacted by Maria Hill who says "SHIELD 616 stand down". Phil Coulson's airplane base is called SHIELD 616
In comic books there are alternate realities and Marvel has numbered each of the known alternate universes. Earth-616 is the name used to identify the primary continuity in which most Marvel Comics titles take place (= our reality). (link)
Mike is now known officially as Deathlok. Deathlok is a known character in Marvel comic books (link).
Random thought... SHIELD is like the FBI for superpowered; super tech individuals. SHILED keeps bad guys in the 'Fridge'. The Fridge was taken over by Garrett (bad guys) and the prisoners were freed. That means that 'Whiplash' (Iron Man 2 baddie) is now free.
The special forces that infiltrate the secret SHIELD base that Coulson and team are hiding in are led by Col Talbot who is a known character in Marvel comic books (link). Coulson recogmizes him and asks 'if I come out will you shoot me?"
Talbot is most know in comic books for being in charge of the military forces in charge of capturing Hulk. Josh Lucas played the character Talbot in Ang Lee's movie Hulk (which is not considered part of the Marvel Cinematic Universe). In 'Hulk', Talbot provokes Bruce Banner endlessly trying to get him to transform into Hulk.
Col Talbot is likely to show up somewhere later to chase the Hulk (in a solo Hulk movie... or in Avengers 2?).
Man-Thing is likely to show up somewhere later. He is one of the escapees from the Fridge that Coulson has vowed to catch. Man-Thing has connections to Dr Strange (who is rumored to be getting a solo movie/franchise soon).