Of all the possible choices to be the "mysterious city" on Marvel's Agents of S.H.I.E.L.D., far and away the most common choice among both our readers and the Internet in general is Atillan, home of the Inhumans.
Whether that turns out to be the case or not, of course, The Inhumans are coming fairly soon to a theater near you, where their bizarre mythology will start to play into the Marvel Cinematic Universe.
Some, in fact, have speculated that we'll see our first Inhumans in Avengers: Age of Ultron, less than six months from now, when Quicksilver and Scarlet Witch are declared to be members of that community of enhanced humanity rather than mutants, as they've traditionally been depicted. For film purposes, mutants are owned by Fox via the X-Men deal.
Inhumans, much like mutants, are a race of enhanced individuals in the Marvel Comics Universe. They were created as a result of experiments by the Kree on prehistoric man. The Kree, of course, are a race who played a significant role in Guardians of the Galaxy and are commonly believed to be the source of the mysterious blue alien body on Agents of S.H.I.E.L.D.
At any rate, with the introduction last week of a mysterious city in the Marvel Cinematic Universe on Agents of S.H.I.E.L.D., quite a few people thought it was possible that we were seeing Atillan, the flying home city of the Inhumans.
Originally an island in the north Atlantic Ocean, it has moved several times, including to off-planet locations like the Blue Area on the Moon and the homeworld of the Kree, Hala. During the Infinity event in the comics, Black Bolt when he detonated a Terrigen Bomb, destroying most of the city, the remains of which can be found within (surprise!) New York, in the Hudson Estuary.
That the whole reason for Infinity was that Thanos had an Inhuman-born child he was seeking puts that villain's importance to the cosmic side of the Marvel Cinematic Universe in an interesting light.