This study will be conducted in two parts. The first part is a pilot study testing the effects of a thalidomide gel 20mg in patients who have developed oral cGVHD-related ulcerative stomatitis following allogeneic bone marrow/peripheral blood stem cell transplant (HSCT). Stomatitis is an inflammation of the lining of the throat and mouth that may lead to ulcers and pain in the mouth and throat. GVHD - a condition in which the donor cells see patient's cells as foreign and mount an immune response to them - may be related to increased levels of a substance called TNF-alpha (TNFa) following HSCT. Thalidomide's anti-inflammatory effects may lower TNFa levels and decrease cGVHD-related stomatitis and oral pain in these patients.