Combine sugar and flour in a medium-size heavy saucepan; stir well. Add eggs and milk; stir with a wire whisk until all ingredients are blended.
Cook over medium-low heat, stirring constantly with a metal spoon, 15 minutes or until mixture begins to thicken and coats the spoon.
Remove from heat immediately, and stir in vanilla. Cool to room temperature. Chill. Pour custard into chilled cups, and sprinkle with nutmeg.