Place shanks in a 12- by 17-inch roasting pan. Bake, uncovered, in a 450° oven for 15 minutes. Add onions; continue roasting until shanks are browned, about 30 minutes longer.
Remove pan from oven; reduce heat to 400°. Add to pan the bell pepper, tomatoes with their juice, broth, pepper, and thyme. Cover tightly; continue baking until meat pulls easily from bone, about 1 1/2 hours longer. Skim fat from pan juices; discard fat. Divide shanks, vegetables, and juices equally among 4 shallow bowls containing hot cooked rice. Add salt to taste.