Like many tools we work with during our practice it's important to always remember to cleanse them afterwards. Cleansing crystals are no different.
Water
While I personally haven't cleansed any of my crystals in water, it is a suggestion but I'll be very careful when cleansing crystals with water. Since it can damage the crystal, sometimes water can eat away at the surface of the crystal or dissolve it. Crystals may also end up changing colour if cleansed in water.
Crystals that are water safe
Clear Quartz
Amethyst
Smokey
Rose Quartz
Snow Quartz
Red Jasper
Soil
You can cleanse crystal with the help of Mother Nature, by burrowing them in soil. This can be a patch of dirt in your backyard or a pot with dirt in it. If you are burrowing crystals outside, I would recommend place something on the spot where you burrow it so you don't forget it. You can leave the crystal for three days or just one day.
Incense/ Sage/ Stick/ Palo Alto
With the smoke of the following four, you can hold the crystal approximately 12 inches away from the source and let the smoke cleanse the crystal. I often work with the method, I find crystals can be a bit picky when it comes to cleansing with smoke. So if you feel as you should stop the cleansing, then you should stop it for the crystal has had enough and is cleanse.
Intention
Intention is a very powerful tool on its own, and can help you cleanse the crystal. I suggest if you use this method work with it as you hold one crystal at a time. You can hold that crystal in the palm of your hand or close to your heart. Picture all the negative away from the crystal, picture white light flowing out of your hand and into the stone. For me, I personally picture smoke wrapping around the crystal, you will know when it is cleansed.
Rice
While I wouldn't recommend rice to everyone since rice can be a bit pricey, depending on what country you may live in. Rice can help, sort of like burrowing it in soil, use a large enough bowl, place the crystal in and pour the rice on it gently. You can leave it for one day.
Sunlight
Not every crystal likes sunlight. Make sure to remember the crystal name before bathing it in sunlight, this way you can look it up and see if you can or cannot cleanse it in the sunlight. Sunlight can do damage and fade the colour of the crystal. Cleansing crystals before practice, in the sunlight may not do it as much harm. Just keep it there for a short couple of minutes, since sunlight is a powerful energy source when it comes to cleansing.
Crystal that don't like sunlight
Rose Quartz
Smokey Quartz
Amethyst
Opal
Sapphire
Beryl
Moonlight
I personally haven't found anything wrong with moonlight, you can wait for the full moon to cleanse your crystal or you can do it no matter the praise. I often leave my crystal on my window still at night and remove them in the morning.
How often should I cleanse them?
Often. Cleanse them quickly after buying them from the shops, whether online or not since crystals will absorb energy around them, cleanse them after practice and if you need to cleanse them before practice.
This is a basic overview on some of the methods out there. I do highly recommend writing the crystal name down, so research can be taken afterwards or if you are anything like me. You may end up forgetting the name, there for forgetting how the crystal is cleanse and having its colour fade away.
There are many methods that one can use to cleanse a crystal. In a way crystals are kind of like people, they have their likes and dislike when it comes to cleansing. In the past I have notice this by feel, if something does not feel right then I won't cleanse the crystal in that method.