Outside method: Place in sunlight (see sunlight chart below), moonlight or rain (see water method) for up to a day. Placing the stone on or near a plant often quickens the process.
Crystal method: If the stone is small small, place it on a quartz or amethyst cluster. The cluster should be dedicated to this purpose with a clear intent. Clean your cluster every month or two in rain or sunlight if possible. Amethyst geodes work well too. This is a great way to clean necklaces!
Sage tea method: This is very effective with less possibility of damaging crystals. Take fresh sage if available and brew a pot of light tea; allow it to cool. Place your crystals in a bowl (use glass if possible) and pour the cooled tea over them. Then remove them and rinse with clean, pure water. Since there are chemicals in most water systems you may prefer to use a gallon of distilled water. If you can safely place crystals outside for nature to cleanse that is perfect, though you'll need to be able to distinguish which stones cleanse best by moonlight and which stones cleanse best by solar.
Smudge method: Pass stones through the smoke of a scented incense such as sweetgrass, frankincense, sage or Dragon's Blood. Passing them through a candle flame also works.
Water method: Place stones under alternating hot and cold running water for 5 minutes (or in the rain for many hours). Place stones in a plastic strainer and then alternate the hot and cold running water from the sink. It is good to have a water filter on your tap to filter out chemicals. This is quick and easy but has drawbacks: some stones loose their coatings when they get wet. Use caution with lapis, malachite and sodalight as they may get damaged faster. Cleaning these stones in the sun or moonlight works fine. [Note: Stones really like the rain. It cleans much better than the usual water method when the weather cooperates.]
Homeopathic method: Some homeopathic solutions clean gemstones as well. Use NET (alcohol-free)
homeopathic to clean stones. Other alcohol-free brands may work as well.
Sea salt method: use 1 cup of sea salt to 2 cups natural spring water. Place stones in the salt, and let them soak for the better part of the day. If the day is sunny, let them dry in the sunshine for a few hours, or if you have lunar stones, lay in the moonlight on a windowsill through the night.
Sand method: when all else fails or you are having a hard time cleaning something, bury it in moist sand (or soil). No wrappings. It will get gems clean but be aware that the polish is often removed when this method is used.
Stones damaged by sunlight (there may be more):
Aventurine: translucent types often loose color
Amethyst: becomes paler
Apatite: pink variety fades
Aquamarine: becomes paler
Beryl: brown or orange types may change to pale pink
Celestite: fades in direct sunlight
Citrine: may change color
Fluorite: green and purple types change color
Rose Quartz: becomes paler
Smokey Quartz: becomes paler
Kunzite: becomes pale or loses color
Sapphire: should be cleansed in moonlight