I'm shocked no one has mentioned Ender's Game yet. In this great book by Orson Scott Card, a young boy named Ender is recruitted to save humanity from a race of hive like alien beings. Military strategists have figured out that if they can destroy the hive mind the "drones" stop functioning entirely. The trouble is, actually getting to the hive mind itself. In order to combat the aliens, Ender is trained to fight and command the entire human army by first controlling a single fighter, then a small squadron of ships, until he is eventually controlling the entire armada. I don't want to ruin the book in case you've never read it, but if you haven't ... I DEFINITELY recomend it.

And yes, City of Lost Children to a degree, but that film isn't really about "controlling" thru clones as it were, more using the dreams of children as an alternative fuel source. And yes, it's a very good film. Similarly you could argue the aliens in Dark City perform a similar role but they're less about controlling the people in their expirament and more about putting people into what they consider interesting situations and seeing what happens.