When you cleanse a crystal or stone, you remove the negativity from it.  As you cleanse it, hold the intention that all negativity will be washed away and the crystal reenergized. 

Different cleansing methods are:

1) Placing it in Moon Water (rainwater that has been left under the full moon)

2) Placing it in a bowl of Sea or Rock Salt
3) Putting it in Salt Water (using sea salt and distilled or spring water)
4) Held under running water like a Stream or Brook
5) Rubbing it with the herb Mugwort
6) Putting in under the Moonlight which can also recharge the stone

7) Passing it through the Light of a Candle
8) Passing the stone through the Smoke of a sacred cleansing Herb or Incense such as Sage, Cedar, Sweet Grass, Copal, Frankincense/Myrrh, Lavender, Cinnamon, Cloves or Juniper.

9) By burying it in the earth. 

A few crystals never need cleansing such as Citrine, Kyanite, Azeztulite, and Moldavite. Some crystals can cleanse others by placing the stone on Clear Quartz and Carnelian. 

(Please note that some crystals and stones should not be cleansed with water as they are water-soluble like Selenite. Sea salt will absorb the water content of Opals which makes them iridescent.

Some crystals can pale in the sunlight like Amethyst and Rose Quartz. It is best to do research on which cleaning method is best for your crystals and stones).

Charging Crystals and Stones:  Push positive energy and reprogramming it to what you want to do with it.  Leave it under the full moonlight or sunlight.
(Amethyst and Rose Quartz should not be left in direct sunlight as the color of the stone will fade)

Books For Reference: The Crystal Bible - Judy Hall; The Complete Crystal Guidebook – Uma Silbey;
Magic of Reiki – Christopher Penczak