In nature, crystals are always transmitting their energy. When we use them, we drain them. Like a battery, they need time to be re-charged before we can re-use them. There are numerous methods cited for the cleansing and clearing of gemstones.

Earth Method
You can bury your stones in the ground (clearly marked area) for a 24 hour period. Apartment dwellers can reap similar benefits from burying the stones in organic potting soil for the same time frame. Note: Do not use for iron based stones such as Hematite and Tiger’s Eye.

Pyramid Charging
The Crystal Pyramid is designed to focus positive energy within, which is best for revitalizing your crystal. It also deflects negative energy up and away which is good for your home environment. The brass used is 90% copper so that the energy flows freely inside. Since the crystals are being charged with positive energy, they are also being cleansed of their negative energy. Generally, crystals are worn or carried near the body to access their energy. When we use these energies, they must be replaced. Pyramid charging is clean, efficient and free, and can be done at any time, in any weather. Crystals that are placed within a Crystal Pyramid will charge quickly and safely without fading or cracking.

Reiki
With Level 1, you can hold the gemstone in your hand and send the universal healing energy to the stone.
With Level 2, you can draw the mental/emotional symbol over the stone.

Sacred Breath
Some like to use this method of blowing away negativity. Simply hold the stone in your hand and blow on it, asking your higher self to cleanse the stone. The stones, in this case, are cleared with intent.

Salt Water
Despite the fact that most books seem to advocate this method, I do not recommend doing so. Crystals do not like salt; it gets into the microscopic cracks in the faces of the crystal, leeching out the water content, leading to dehydration and cracking of the stones.

Singing Bowls
There are Tibetan Prayer Bowls made of metal alloy (looks like brass) that resonate when struck or rubbed along the rim. These bowls can hold many stones at once. They are cleansed thoroughly and quickly (within a minute or so). The sound also has a purifying effect on the surroundings.

Smudging
This is the least invasive and most popular method for clearing gemstones. You can use a smudge stick for this. A smudge stick may consist of some of the following herbs: cedar, sage, lavender, juniper, pine. You can either pass your gemstones through the smoke or pass the smudge stick over them. This method is excellent for clearing yourself and your environment as well. However, you should be warned that sage smells very much like marijuana when it burns.