If momma dog had lots of puppies, chances are she won't be able to feed all of them the same. Either she doesn't have enough nipples, or some puppies just don't have the energy to feed as often or as much as they need to stay healthy and grow. The result? You'll have a runt on your hands. When the mom's unable or unwilling to feed all her puppies, you can fatten up the runts yourself.
Start feeding extra food to the runt while he's still nursing. If he's still too young for dog food or he won't nurse at all, you can buy special formula from a vet or pet store and bottle-feed him "on the side." Don't prevent him from drinking mom's milk -- the formula should just be an extra.
Feed the runt separately from his siblings. Once he's old enough to start eating puppy food -- 3 weeks old at least -- separate him and feed him on his own. This will prevent the stronger puppies from trying to steal his food and causing him stress. Also, the runt might eat slower than the other puppies or might get fuller faster since he's smaller and his stomach can't hold as much food. If that's the case, feed him several times a day to ensure he's getting enough nutrients and calories.
Buy a high-calorie nutrition gel. These are special, calorie-dense vitamin gels. They are designed for animals recovering from illness or surgery but can also benefit pregnant animals and puppies. Ask your vet how much to give the runt, especially if he's very young -- just a couple of weeks old or less -- and his age is not mentioned on the product label.