I would say very few people actually build their own wheels. The vendor that you purchase the carbon rims from will actually build the wheels for you. They can use a generic brand of hubs called Novatech that people seem to have pretty good experience with, or they have a few name brands available, or if you want a certain hub they don't carry you can mail them to the vendor and they'll build the wheel with those hubs; of course that has added shipping costs.
The most popular trends are having the vendor build your carbon hoops up with Novatech or DT Swiss hubs that they have in stock. The Dt Swiss 350 hubs would be my choice and I think most vendors keep them in stock, but they will be a bit more expensive than the Novatech option.