Special stains are used in hematology and cytology to identify specific molecules that are not visible with routine staining. They can determine if certain molecules are present or absent, where they are located, and how much is present. Examples of special stains discussed in the document include fetal hemoglobin stain, Prussian blue for sideroblasts, methyl violet for Heinz bodies, Papanicolaou stain in cytology, and Masson Fontana silver stain to identify melanin and argentaffin granules. These stains help characterize and diagnose blood and cellular abnormalities.