A few things! Muffins typically have a domed top, whereas cupcakes are a bit flatter. Also, muffins also tend to have berries, chocolate, or other ingredients folded into them whereas cupcakes usually do not or are stuffed after being baked. Lastly, muffins are also usually topped with a streusel or glaze or a hint of sugar, whereas cupcakes are typically topped with a frosting.