"Dead man walking" is a phrase that prison guards in San Quentin used to shout when they took a condemned man out of his cell (7.102). So the title refers to Pat Sonnier and Robert Lee Willie, the two men Prejean advises. They're condemned men who are as good as dead, even though they're still walking around. In fact, the title could refer to anyone on Death Row—they're all dead men walking.
Kind of gruesome, huh? There's also a less grim reading of the title. Sonnier and Willie were already dead by the time the book was written—but in the book they walk, they talk, and they are remembered. So Dead Man Walking could refer to the fact that the book tells the story of people who are dead, and tries to be sure they are remembered. In this reading, the dead walking might not just be Sonnier and Willie, but their victims, whose families and lives are also remembered in the book.