I just listened to all of the songs again. The Waits one is definitely my clear favourite, and Steve Earle's version is last for me, but second place to fourth is surprisingly unclear. I think it goes Blind Boys, DoMaJa and Neville, but I like the percussion of the Neville version very good, even if the rest of the song is a little weaker. I'm sticking to my season ranking of 2, 1, 4, 3, 5 of last year, but the three middle ones are close to interchangeable for me, for vastly different reasons.
Now, I know that the same theme song in different versions is done on other shows as well, but I think it's incredibly appropriate for The Wire, considering that one of the major themes is "same shit, but different".