I'd bet Benjamin that it's the MoM's heart. Really think about how heartless, and more especially, nobodies are created. The MoM fades away, he says so himself at the beginning. "I'm going to fade away," he says. He doesn't die. When the heart leaves the body, a heartless is born from the heart, consumed by the darkness. The body "fades away" and a nobody reappears somewhere else. But in order for a nobody to be created, a heartless must be created with it. It's all in the Ansem reports. So why didn't the MoM become a heartless and form a nobody? Thaaaaat's the whole purpose of the box. It's black, like the cloaks. And any KH fan worth his/her salt knows what the cloaks are for. The MoM used the box to protect his heart from the darkness, thus keeping himself from becoming a heartless. And since no heartless was created when his heart was removed, no nobody reappeared anywhere else when his body faded away. And what's inside that box is another key... THE key to resurrecting the MoM, which we will probably see in KH3.