most people use crystals the same colour as the chakras.......
crown (purple) - amethyst
3rd eye (indigo) - lapis lazuli
throat - (blue) blue lace agate
heart - (green/pink) rose/qu or any pale green
s/plexus - (yellow) citrine
sacral - (orange) carnelian
root - (red/black) jasper, haematite, tourmaline etc.
but some folks use clear qu at crown and amethyst at 3rd eye so use what you feel most comfortable with