I've recently had a single speed built by my local LBS, they were great. Took the frame and forks to them and they did the rest, all i had to do was chose the components etc.
I'm stoked at the ride, now I use it for the commute to work.
LBS is the way to go to get the wheels built up, but tracking down hubs is a different matter. Pending if it for road/MTB you only have a certain about of options for each....