The method you use is always a matter of personal choice. Approach the crystal as if it is a living entity. Most people wash their crystals in water or soak them for several hours in sea salt mixed in water.
Here's another method, which may seems silly to some - but it works for most crystals. Use a liquid soap - such as "Soft Soap".
Rinse the crystals - apply a bit of soap - rinse them gently again - and then place them on a soft cloth to dry. Next, place them on the window sill to allow the sunlight and moon light to energize them.
Here are several other good methods to clean your crystals:
Water Cleansing
Take your crystals to a natural source of water, the ocean, a waterfall, a spring or a stream and immerse them in the running water. If you have no natural source nearby then bottled spring water can be used as a substitute. Allow them to dry naturally, preferably in the sun as this will re-energise them. Never dry them with a cloth.
Salt Water Cleansing
Do not allow your crystals to come into direct contact with salt. It may damage the structure of the crystal as well as damaging the polished finish. It can even cause colour changes. For example, if opal is placed in salt, the salt draws off the water from the opal and changes it into chalcedony.
By far the best way to cleanse with salt is to fill a dish with salt and cold or tepid (never use hot) water and place your crystal in another smaller dish standing it directly in the water. The fact that it does not have direct contact with the water will not affect the cleansing process.
Earth Cleansing
Bury your crystal in the garden (make sure you remember where)! and leave it for 24 hours. Do not bury in acidic soil which can cause damage. If you don't have a garden, a planter pot will work equally as well. After 24 hours, rinse the crystal in pure water and leave to dry naturally.
You can also cleanse your crystal by burying it for 24 hours in a bowl of uncooked brown rice. This is just as effective but discard the rice after and do not eat it.
Fire cleansing
Surround your crystal with tea light candles (on a safe surface do not leave unattended) and burn them until the candles die out naturally. You can pass your crystal through the flame, however, don't do this with Opal as again, it can cause damage.
Smudging
Smudge sticks are bundles of tightly bound plant materials. This method played an important role in North American Indian tradition. A good smudge stick to use is Sage as it can not only cleanse your crystal but dispel negative energy from a room and clear an aura too.
Light the smudge stick and then blow it out until it is just smouldering. Waft your crystal through the smoke ensuring that every part is treated.
Cleansing with other crystals
A good way to cleanse is to place your crystal on a bed of quartz crystal or amethyst druze or cluster. This negates any negative energy after a few hours.
Flower Cleansing
Choose flowers that appeal to you or are like the stone in type. For example rose petals for rose quartz, or lavender for amethyst. Bury your crystal within them in a clear jar and leave for 24 hours. If possible, also then leave in the sunlight and moonlight for 24 hours to re-energise it. A full moon is particularly effective.
Cleansing with Essential Oils
Dab a drop of essential oil onto a cloth and rub over the surface of the crystal. Alternatively, use essential oil in an oil burner and pass the crystal through the vapour whilst the oil is being heated. A dab of essential oil directly onto the crystal can enhance the oil's fragrance and act as a room freshener.