1. A method of treating a patient with an autoimmune disease or chronic immune system disorder, comprising the steps of: administering a therapeutically effective amount of an anti-CD40L compound to the patient for a first therapeutic period, in doses separated by intervals of less than about 3 weeks; and then administering a therapeutically effective amount of the anti-CD40L compound to the patient for a second therapeutic period, in doses separated by intervals of at least about 3 weeks. 2. The method of claim 1, wherein the disease or disorder is selected from: systemic lupus erythematosus, myasthenia gravis, autoimmune hemolytic anemia, idiopathic thrombocytopenic purpura, anti-phospholipid syndrome, psoriasis, an allergic condition, arthritis and multiple sclerosis. 3. The method of claim 1 or 2, wherein the anti-CD40L compound is an antibody or antibody fragment. 4. The method of claim 3, wherein the antibody is a monoclonal antibody. 5. The method of claim 4, wherein the monoclonal antibody is 5c8, produced by hybridoma ATCC HB 10916. 5. The method of claim 1 or 2, wherein, during the first therapeutic period, doses are separated by weekly intervals. 7. The method of claim 1 or 2, wherein, during the first therapeutic period, doses are separated by intervals of two to six days. 8. The method of claim 1 or 2, wherein, during the first therapeutic period, doses are separated by daily intervals. 9. The method of claim 1 or 2, wherein, during the second therapeutic period, doses are separated by intervals of at least about 4 weeks. 10. The method of claim 1 or 2, wherein the therapeutically-effective amount of the anti-CD40L compound is an amount sufficient to prevent deterioration of the patient's medical condition. 11. The method of claim 1 or 2, wherein the therapeutically-effective amount of the anti-CD40L compound is an amount sufficient to cause improvement in the patient's medical condition. 12. A method of treating a patient with an autoimmune disease or chronic immune system disorder, comprising the steps of: administering a therapeutically effective amount of an anti-CD40L compound to the patient for a first therapeutic period, in at least four doses separated by weekly intervals; and then administering a therapeutically effective amount of the anti-CD40L compound to the patient for a second therapeutic period, in doses separated by monthly intervals. 13. The method of claim 12 wherein six doses of the CD40L compound are administered during the first therapeutic period. 14. A method of inhibiting rejection of transplanted tissue within a patient, comprising the steps of: administering a therapeutically effective amount of an anti-CD40L compound to the patient for a first therapeutic period, in doses separated by intervals of less than about 3 weeks; and then administering a therapeutically effective amount of the anti-CD40L compound to the patient for a second therapeutic period, in doses separated by intervals of at least about 3 weeks. 15. The method of claim 14 wherein the transplanted tissue is an allograft or a xenograft. 16. The method of claim 14 wherein the transplanted tissue is selected from: skin, kidney, liver, heart, bone marrow, and eye tissue. 17. A method of suppressing an immune reaction to a transgene product, following gene therapy of a patient, comprising the steps of: administering a therapeutically effective amount of an anti-CD40L compound to the patient for a first therapeutic period, in doses separated by integrals of less than about 3 weeks; and then administering a therapeutically effective amount of the anti-CD40L compound to the patient for a second therapeutic period, in doses separated by intervals of at least about 3 weeks. 18. The method of claim 1, 2, 12, 14, or 17, wherein the patient is human. 19. The method of claim 1, 2, 12, 14 or 17, wherein the anti-CD40L compound is a humanized anti-CD40L antibody.