There are many methods used by different crystal workers for cleansing and clearing their crystals and healing stones. These are some of the methods that have been found that work.
Cleansing your stones under running water
Make sure the water is not too hot or cold so that any natural cracks in the stone are not exacerbated by the effect of the water. If you live near a river or stream, all well and good, but otherwise tepid tap water will be just as good. Hold your stone under the running water for a few minutes, and while concentrating on it's energy, ask for all the negative and unharmonious vibrations and energies to leave and only those that are beneficial and positive to stay. Gently dry your stone with a cotton towel. It is then ready to use.
Smudging With Incense
Some healing stones, such as calcite, selenite and dioptase will crumble or cleave on contact with water. With these stones, use incense for cleansing. Sage and Cedar (used by native americans) and sandalwood are the best, because they are cleansing substances, although many sandalwood-based incense will suffice. Surround your stone with the cleansing smoke of a smudge stick ir incense stick, while asking for it to be cleansed of any negative or unharmonious vibrations and energies.
Placing on a Cluster
One easy way of cleansing your stones is to place them on an amethyst or clear quartz cluster, They can use the cluster as their permanent home. Amethyst in particular has cleansing properties. Clear Quartz will assist your stone in building up it's healing energies.
The Sun and the Moon
Crystals and healing stones enjoy sitting in the sunlight and moonlight. They will be rejuvenated and cleansed. Remember to keep water sensitive stones out of the rain. You may wish to place them in a window which receive much sunlight or moonlight.
Burying In the Ground
Bury your stone a couple of inches below the ground, remembering where it is! A terminated crystal should be placed with the point down. Visualise cleansing and healing energies going into the stone. After 24hours, unearth your stone. If it feels like it needs more time, rebury it, keeping an eye on it until it is ready to come out and be used for healing work. This is a good method for stones that you haven't managed to cleanse and clear with either the water or smudging methods. (Don't use this method for water sensitive ones incase of rain!)
Now, I shall give you a list of Crystals and Healing Stones from A-Z and what they help to heal.