Pekin ducks account for about 95% of the commercial meat duck market in the US. Muscovy ducks account for a little more than 3% in the US. However in France, 60% of the ducks raised for meat are muscovy. Then there are the muscovy/pekin crosses that account for a large percentage of the meat ducks in Taiwan.
Personally, I enjoy the pekin duck. I render the duck fat and use that to fry potatoes and vegetables. The muscovy duck does not lend itself well to rendering being a leaner duck. One of our customers, the head of the culinary department at a fair sized university bought one of our muscovies and was disappointed that he did not get the fat that he had heard so much about from other chefs. He now has placed an order for two pekins, which we plan to fatten up on corn for the last couple weeks. Another customer wants wild mallards, which are really small ducks. He prefers the gamier flavor.
Pekin are also nice in that they are prolific layers, and the eggs are easy to incubate. However, you can't really go wrong with either pekin or muscovy.
One other thing is to try to get white ducks. The carcass looks much better after plucking.