I've never been into 'smelling' my puppies (other than I love the smell of new puppies ...) but I'd suspect they all smell the same to a human, when in the nest. Given that bitches do know if there's something wrong with an individual puppy, pushing it to one side, I suppose a dog might smell something off with a puppy. To support this, if a b itch is needed to foster a litter if their mother has died, all the puppies have to be marked with the scent of the foster mum so she accepts them as her own.
Once out in the world, they take the smell of where they live and their individual smell. A lot depends on food eaten, and environment, once not in a litter.