I have a new Halo 3 theory. It came to me while playing the level "Regret." Maybe the three main prophets live up to their names...
Regret: During the water ride in the level Regret, Cortana talks about how Regret "jumped a gun" by attacking Earth, and apologized to the other two prophets. He "regrets" attacking Earth.
Mercy: In the next water ride, Cortana (quoting Truth's message to Regret) says that Regret will "be spared a public view of our contempt thanks to Mercy and his wise counsel." Mercy showed mercy to Regret.
Truth: Of his name's meaning I am not sure of... maybe he knows the truth about Halo, and for some reason still wants to activate it.