While I suppose MODOK is a classic, it strikes me as more likely at this point that what they are dealing with is "The Chaos Computer" if it is a mathematical/computer based precognitive device. "The Chaos Computer" would be well timed with other events in the Marvel Cinematic universe going on right now, as well as being an obscure enough reference where it would take people by surprise while still being canon enough to say "this was always out there".
For those unfamiliar with it there was a team in the 1990s called "Force Works" largely run by The Scarlet Witch and Iron Man. They broke off from the Avengers team to take a more pro-active approach, using the aforementioned "Chaos Computer" to predict problems before they could happen and head them off. While the computer was powerful on it's own, to really function at it's true potential it needed The Scarlet Witch to use her own probability manipulation powers in conjunction with it. This team didn't stay around too long but a new version of it was hinted as operating behind the scenes for quite a while now:
http://en.wikipedia.org/wiki/Force_Works
The reason this seems likely is because Iron Man is the biggest apparent cash cow in the cinematic universe and just about everything seems to revolve around "Starktech" probably because we don't have anyone competing with him like say Reed Richards for "smartest dude out there known to the public" at least at the moment. Him ultimately having invented whatever this is, or at least started out the concepts, makes a degree of sense. What's more it provides something they can later pull out when "The Scarlet Witch" is apparently introduced (if rumors are true) as a sort of last minute ex-deus machine, having set it's existence up on "SHIELD" and being able to use it to justify her predicting and heading off events retroactively. It making sense that a powerful, if flawed, device in SHIELD, would suddenly become that much more powerful in her hands as that's how things worked out in the comics.
Depending on where things go, this also opens the door for them to also do a "Force Works" series at some point, using "B" and "C" list characters since it's semi-open for who is members, and could be justified as doing almost anything. "Force Works" considered by some as one of the most awesome concepts that never really made it, and remains as something of a cult classic with Force Works characters still tending to be ones associated with Iron Man and his circle, and even used as his backup (replacing US Agent with Hawkeye) in the older Iron Man cartoons.
I'm probably wrong, but that's my immediate guess, in a similar direction to Bob... and in part backed because since SHIELD seems to be trying to avoid doing too much with actual super-heroics, probably due to budget reasons, actually making MODOK would probably be beyond them... unless they used most of their FX budget for it, and really something that silly would probably be a bad idea.
Though if Bob is right, and they do introduce Modok, we should demand an "Agents Of H.A.T.E." inspired episode where the team winds up infiltrating a warehouse defended by a bunch of Elvis impersonating MODOK clones that attack by throwing hamburgers....
