"Stagolee Shot Billy" by Cecil Brown is an interesting book that traces the history of the blues song from a real-life incident in late-1800s St. Louis to its impact on rap today with lots of discussion about its cultural context and meaning. The latter got a tad too acacdemic for me in places but not to the point of being painful.
While reading the book, I've been collecting versions of the song from emusic and other places. But my favorite versions are on CDs I already owned: "Stack 'O Lee" on the Mississippi John Hurt CD "Avalon Blues: The Complete 1928 Okeh Recordings" from Columbia and "Stack-O-Lee" on the Champion Jack Dupree CD "Blues from the Gutter" from Atantic. I also like Sidney Bechet's instrumental version "Old Stack 'O Lee Blues" from Blue Note's "The Best of Sidney Bechet," available as a single at the iTunes Music Store.