M.O.D.O.K. appeared as a boss in Iron Man 3: The Official Game, a mobile game tie-in to (you guessed it) Iron Man 3:
In the game, he's an enhanced version of Aldrich Killian, the main antagonist from Iron Man 3 and founder and CEO of Advanced Idea Mechanics (A.I.M.).
Obviously the canonicity of video game tie-ins is questionable.
Christopher Markus, writer of the Captain America franchise, has expressed interest in bringing M.O.D.O.K. into Civil War, as he said in an interview with SFX, but finds it unlikely that it'd be approved:
SFX: You managed to get Batroc and Sharon Carter into The Winter Soldier. Were there other Cap characters you were keen to bring to the screen but couldn’t quite fit into the second film?
CM: I don’t know if there’s anybody that we had in the wings that we couldn’t pull off. There are people that I’m always wanting to bring in. I want to put Modok into something, but you can’t just drop a giant floating head in! It’s not like “Oh, we have to go talk to this guy – there’s something I should tell you about him first…” [laughs]. Suddenly the whole movie needs to take on that structure in order to accommodate him. I never win that fight!
If there are any more substantial plans, I can't find any comment from Marvel.