It always used to be Merlin BITD, but they've no doubt lost out to Chain Reaction over the years.
It's just a matter of volume. There's no way your LBS can compete with a workshop that's churning out wheels all day. At the LBS it's all about reminding yourself how to do it, finding the tools, have we got any spokes in stock, buying spokes, rims and hubs in small volumes and low discounts. The cost is doubled in no time, and the quality is no better, if anything worse.
I think I'd still go for Merlin, but perhaps only because that was the thing BITD and this is Retrobike.
I've used Merlin in the past and the wheels were very good - I had a quick look but they don't have the hub that I want (Sun Ringle Disc Jockey - its half price at CRC too).
One of the LBS's don't even bother having a full time builder, just a guy who comes in one day a week. His wheels are pretty darn good too - its just a bit slow.
2015 Stanton Ti Switchback
2006 Specialized Demo 8
2013 Specialized Allez Sport
1999 Santa Cruz Chameleon
1994 Cannnondale Beast of the East (rebuild still in progress)