The Jew of Malta. Pretty straightforward: Barabas is a Jew who lives in Malta.
But you know what? We're pretty interested in that little "of Malta," there. In Barabas's Character Analysis, we talk about how he doesn't really belong anywhere. (Missed that? Check it out and then head back.) Jews aren't allowed to be full citizens, so Barabas is an "alien."
But not in the title. In the title, he's the Jew "of Malta." He belongs to Malta, even if Malta doesn't want to admit it. And that makes us think that Marlowe is suggesting that Malta is partly to blame for how Barabas is. Maybe Barabas is such a psychotic killer because his status as an outsider has forced him into it. If Malta were a more open, accepting community, Barabas would never have been forced into his murder spree.
And one more thing. In 1633 quarto (i.e. the first published version of the play) the title page reads "The Famous Tragedy of the Rich Jew of Malta."
Check it out: