I was at the first three shows of this leg, which includes Stockton. There wasn't much variation in the songs performed, but it seemed as if Bob really wanted to focus on the songs he had chosen and get their meaning across in the right way.
As far as She Belongs to Me, the downsinging began in Reno a few nights before, and after Stockton it continued into Santa Rosa. I think Stockton is the most enjoyable of the three. Actually, Sotckton is one 06 show I often revisit on recording. The entire show comes off solid on boot. Maggies, Lonesome Day Blues, Highwater, and Till I fell in love are notable performances.
Agreed about the "Timber" voice of early 06. If that she Belongs doesn't suffice as an example, just listen to this Till I fell in love from Stockton
http://www.yousendit.com/transfer.php?action=download&ufid=E971F44758242980 . I love Bob's attitude on this one, how he sorta talks his way through. And listening to these early Herron-Freeman shows, you can really hear how much they've changed over the years. back then they were much more of a conventional band - taking individual solos in a more flashy, prevalent manner.
Also, Reno was when the organ first appeared. I remember in the opening Maggie's something didn't sound quite right, everything was more circus-like. It took a few verses to realize what was going on.