Here are the stones I associate (and use) with the seven major chakras.

Crown:
All white stones. Quartz, primarily. Moonstone might also be used, but not for high power situations (I find moonstone to be a bit ‘soft’ in its energies.)

Third Eye:
All purple stones. Specifically, Amethyst, Iolite, Azurite, and Flourite (specifically when working with the upper chakras, or when attempting to meld emotion and reason).

Throat:
All blue stones. I personally like Lapis Lazuli and its less-expensive sibling Sodalite, a coven sib prefers Turquoise, and another prefers Aquamarine. I feel that the color/stone chosen reflects the wearer’s need for specific energies for this chakra.

Heart:
All green and pink stones. Emerald is the most famous (and expensive), but I prefer Malachite and Aventurine. Bloodstone is a powerful stone to use (with caution) as it can connect the heart to the root and produce powerful transformations. Jade is good to work with when connecting the lower and upper chakras. Also Labradorite. Rose Quartz is a gentle opener.

Solar Plexus:
All yellow stones. Citrine is particularly wonderful – I hang mine on a long silk cord so it is at same level and the energies are strongly linked. Amber is another fantastic stone to use with this chakra, as is (yellow, not smoky) Topaz. Some people like Peridot, particularly when working with linking the heart to the will.

Belly:
All orange stones. Carnelian is powerful, as are some colors of Jasper.

Root:
All red stones. I particularly like using Garnet, Bloodstone, and red Jasper

Clear (quartz) or black (obsidian) stones can be used on any chakra to help open, clean, or close the energy flows as part of the healing or balancing process. NEVER open a chakra wide and leave it; alternatively NEVER completely CLOSE a chakra. Too open or too closed produces an energetic imbalance.

~from Maat's Book of Shadows