Any surface that rainfall is collected from impacts the quality of that water. We want to avoid chemicals and contaminants. If the surface is toxic so will be your water, if the surface is dirty so will be your water.
Wood Shake (most are treated with brominated fire retardants)
Galvanized Metal (unless info is acquired from the manufacturer you should assume cadmium is used in the coating)
Asphalt Shingle (PAHs and Fire retardants, excess sand)
Any product rated NSF61
Metal roofing epoxied or enamelled coating
Galvalum Metal roofs
EPDM without fire retardents