In the Lost episode "The cost of living", Mr. Eko is surprised that the corpse of his brother Yemi has disappeared. What happened with it?
It's a solid fact in Lost that The Man in Black has morphing ability. I think the narrative of what happened leading up to Mr. Eko's death leaves little doubt that the Man in Black had either removed, disposed, or taken control of Yemi in order to manipulate Eko (from Lostpedia):
However, Eko found that his brother's body was no longer in the plane. Eko saw Yemi once more appearing in dirty clothing and chased him into an open field. There, Eko confessed that he had not sinned to his brother. Eko stated, he did not ask for the life he was given, but it had been given nonetheless. And with it, he did the best he could. Eko also mentioned his sacrifice for Yemi when they were young.
Eko delivers his last message before his death. However, what appeared to be Yemi announced, he was not Eko's brother. Then, the person who appeared like Yemi disappeared into the jungle, with Eko in hot pursuit.
The manipulation would not have worked as well if the body would have still been in the plane.