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Amethyst- (crystal purple/white) this stone is used for spiritual upliftment, this stone is also very grounding and calming.  It's also ideal for communication and Balance.
Aventurine- (Green, Blue or Red with metallic specks) This Stone is ideal for physical healing, I wear this stone around my neck when I have a sore throat, or on whichever place needs healing.  This stone is the one I would choose for an over-all healing. It is also a good luck stone. Aventurine is sometimes called Indian Jade.
Agate- All agates are very grounding, and aid in protection, and attraction.
    Fire Agate- (clear flame colored) can alleviate pain.  stimulates awareness.
    Silver Leaf Agate-  (milky with silver or green threads or plumes) they open the wearer for acceptance, abundance and protection.
    Lace Agate- (milky with red ‘plumes’) this stone balances physical energies, and can help you to reach high physical levels.
    Moss Agate-  (milky with green ‘feathers’ or lines) Provides healing and growth, it also helps self-esteem and emotional balancing.
    Banded- (layers of color (blue, red, or brown) and clear) all over healing. be careful, a lot of the time, these stones are not natural
Alabaster- (opaque white to cream) facilitates forgiveness, astral travel, and is useful in treatment of disorders of the heart.
Amber- (clear/smoky brown, orange, yellow or green)  wonderful healing stone though in fact it is fossilized tree sap.  soothing to the nervous system, and is compatible with all Chakras.
Azurite-  (bright clear blue) Assists is dissolving egoism, conceit, arrogance, and vanity.  It calms anxiety and facilitates rationality.  It provides insight and stimulates the third-eye.
Bismuth-(silver white to red) can aid in transformations and physical vitality.  if used properly it can be used to ease fevers.
Bloodstone- (green with red flecks) Intense healing stone. can stop minor bleeding if placed on cut.  adds courage, and can dispel bewilderment.
Calcite- (any milky color) energy Amplifier  and aids memory.   
Carnelian- (clear red or orange) this stone Balances creativity and mental processes.  It's useful when undertaking any project.  It's an Ideal stone for use with the sex/navel Chakra, and is the bearer of the orange color ray.
Cinnabar- (opaque red to dark orange, other colors are Man-dyed) Stimulates dignity, vitality and power.  it is said to attract money as well as the ability to maintain wealth.  this stone transmits the feeling that "everything is indeed ok"
Citrine- (clear and yellow) This stone's for Upliftment.  I wear this stone when I have back problems.  It's the bearer of the Yellow Color ray, and is used with the Root Chakra.
Cobalt- (steel grey with violet/blue hues) best used for creative endeavors.  it is also regarded as a heal all
Emerald- (clear green- any shade) {side note, the so called 'red emerald' is in actuality NOT emerald but Bixite though both are varieties of Beryl} Emerald is known as the stone of 'lasting love'.  Emerald helps combine thought and correct action.  this stone is also a wonderful focus stone.
Fluorite- (layered clear blue, pink, purple, or green) this stone's for hormonal balance.  I use it when I need relief from PMS.
Garnet- (dark red, to purple) Garnet is a stone of maintaining health.  it will discourage chaotic, sporadic, and disruptive growth both physically and spiritually.
Hematite-  (metallic Black) This stone helps to 'sort out' things in one's mind and is ideal for mental attunement, memory enhancement, original thinking, and technical knowledge.  It is said to attract love, and bring peace, self-control and inner happiness. It is also thought of as a healing stone since if it is scratched it will 'bleed'. the rust colored mark will disappear in a few days.
Jade- (many shades of green, white, tan, and/or clear), This stone brings relaxation.  I wear this stone when my shoulders are tense, and I've found I'm much calmer
Jasper- This stone helps bring what one needs, which may not be what one wants.  It's a wonderfully supportive stone.
    Poppy Jasper- (light spots, on dark) This type of Jasper helps one gain a more positive outlook.
    Leopard Jasper- (dark spots on light) this jasper has similar properties to poppy jasper and red jasper.
    Red- (dark red to brown) defense, Night Magick, stress relief.
    Green- (any shade of green) a good over all healing stone.
Labradorite- (grey, yellow, black, white with a spectral sheen)  Astral Projection, meditation, facilitates the transformation of intuition into intellectual thought.  it symbolizes celestial bodies.  this stone can help unite body and mind, as well as help balance them.
Lapis Lazuli/ Sodalite-  (lapis is rich royal blue, sodalite is royal blue with white lines) these stones are for Understanding, and protection, against negative forces, be they Spiritual, Emotional or even Physical.  I wear one of these stones over my heart Chakra when I need my heart and mind to be in balance.
Malachite- (light to dark green, usually banded) another stone of transformation.  Facilitates insight and meditation.  this stone is an equalizing and balancing agent. 
Moldavite- (light clear green when kept in the dark, but will darken to almost opaque black when left in the sun) Moldavite is the only gem quality Tektite (meteor fragment) this stone stimulates inter personal relationship of any kind.  it also stimulates the third eye chakra as well as the throat Chakra.
MoonStone- (milky white, pink or blue with silver flecks) promotes love, compassion, and sympathy. 
Obsidian- (clear black, opaque black, or black with white spots.) This stone is for grounding excess energy.  I gaze into this stone for a short time (1-2 mins.) for 3 days when I need insight to a particular problem.
Onyx- (black, black and white, brown and white, honey and white) This stone helps to change bad habits (if you really want them to change) it's great when used as a necklace.  It's also a wonderful grounding stone.
Opal- (white with spectral flecks) This stone is excellent for seeing possibilities, and helps one to see a problem from all angles.
Pyrite-  (metallic gold, 'grows' in cubes) Harmonizes energies, improves circulation, and eases anxiety.  It’s said to be a 'money magnet' and it shields from negative energy.
Peridot- (Clear pale green to yellow) this stone emits a warm friendly energy, it assist in understanding and identifies detrimental patterns.  It can act as a shield around the wearer against physical danger
Quartz-
    Clear Quartz-  (clear) this is the universal Stone, it can be used with any Chakra, and it is an extremely powerful crystal.  It can hold a lot of energy, and is a wonderfully soothing stone.
    Rose Quartz- (clear rose pink) This crystal is for emotional balance, it's an excellent stone to wear when you need to express or soothe your emotions.
    Rutilated Quartz- (clear with dark brown or black lines inside) Assists one in getting to the root of a problem, and helps assess the reason for a disease or discomfort.  It stabilizes relationships and heightens love and strength. It also aids growth through reason and order.
    Smoky Quartz- (clear black or brown [like soot]) Protection while traveling.
Ruby- (bright clear red to deep opaque red, 'grows' in squat octagons) this stone is for the Emotions, especially Love Passion and Lust.  They help one to open their heart, and see through many problems.
Sapphire- (light to dark clear blue) this stone is for mental clarity.  It's helped me to study for more than one test. And ideal way to use this stone, is: When you're feeling confused, or mentally tired, hold the stone up to a candle's flame, and gaze into the stone, asking for clarity..... It will soon be granted.
Serpentine- (green, black-green, brown-red, brown-yellow, and white)  can be used to clear all chakras.  can help to remove parasites from the body and cleansing the blood. 
Spinel- (clear red, blue, violet, black, green, yellow orange, brown, and white) in addition to having the properties of their specific color, Spinel offers encouragement when dealing with difficult things.  it is known as the stone of Immortality and beauty.  this is a wonderful stone to use on the appropriate color Chakra. 
Sunstone- (clear orange, or opaque white with orange and gold flecks) this stone helps clear one's thoughts.  I've found that this stone is extremely helpful when I meditate; my vision is always sharper, and more enlightening. (This stone is best paired with Moonstone)
Tiger's Eye-  (Honey brown with banded clear sections , very rarely blue or green with clear bands) Brings clarity and enhances psychic ability; it can help discipline sexual/emotional life and allow one's life to blossom.  It brings protection, practicality, and softens stubbornness.
Tourmaline-
 Watermelon Tourmaline- (translucent green on the outside, red or pink insides, 'grows' in long octagons) this stone is unique in that its colors blend from bright green on the outside of the stone to a soft pink or red on the inside.  This color blending is ideal for balance (since red and green are opposites on the color wheel) Use this stone when you need to balance your heart and mind.
    Black Tourmaline-  (clear to opaque black) This stone is best used when you need strength, for any undertaking.
Topaz-
    White Topaz-  (looks much like a diamond) this stone has the same properties as Quartz and Diamond.
    Yellow Topaz- (from pale yellow to honey brown) this stone is best for physical healing, as well as protection while traveling.
    Orange/Brown Topaz- (honey brown to medium orange) Transforms negative energy into positive.
    Blue Topaz-  (pale clear blue) this stone's best for communication.
    Pink Topaz- (pale clear pink) This is a very peaceful stone, and will aid in sleeping, and help you to remember your dreams.
Turquoise-  (opaque pale blue though rarely found in green, looks like chewed bubble gum) a highly absorbent stone, it will drain of color if in contact with your skin while your highly stressed the color will return after you've relaxed for a while, or after extended time away from your skin. (Unfortunately, most turquoise on the market today is coated with a clear enamel to prevent 'bleaching' and this particular attribute is seldom seen) A master healing stone.  It promotes spontaneity in romance and stimulates the initiation of romantic love.  It balances and aligns all Chakras, and can bring all energies to a higher level.  A highly spiritual stone, yet grounding.  It brings soothing energy, peace of mind, strength, wisdom, protection and positive thinking.

Cleansing Crystals
There are so many ways. Which change due to the crystal or metal you are working with.  Generally, at least one of these methods should be done until the stone FEELS clean. To 'see'  if a stone is clean, simply hold the stone and relax and use your inner awareness to get a feel for the stone.  if the reaction is cool and neutral, the stone is clear.  However, don't be upset if the first time you try this and it doesn't seem to work, it just takes a lot of patience, and practice! the next step in cleansing a stone is  asking the elemental spirits (corresponding to the method you choose ie a water Elemental for any water method, etc.)

Sea Salt and water-  only use this method if you are cleansing a stone that will not be damaged by water (like Pumice, mica, Moldavite) all you have to do is fill a bowl with clean water  and a little salt, and place your stones in the bowl.  Leave them there for 3 (6,9) days (minutes, hours) {the longer the better} after asking the spirits of earth (salt) and Water to cleanse the crystals of any negativity or anyone else's imprints.

The sea-  Next time you're at the beach, try placing your stones (as long as they won't be affected by the water) in a net, and submerging them in the water, if you feel it's safe enough, secure the net to some rocks, or other stationary place, and leave them there.  If not, hold the net (or lacking a net, loosely in your hand) until you feel the stones are clean.

Rivers or lakes - Basically, this is done the same way you would in the sea. This is an excellent way to cleanse your crystals.

Smudging-  You can do this with either a Sage smudge stick, or  clove, sandalwood, cedar or rose scented incense. Hold your stone loosely in your hand, and pass it through the smoke at least 3 times.  Though I personally do this till the stone FEELS cleansed.

Burying in Earth or sand- This is my personal favorite.  You should cleanse the area you wish to bury your crystals in before hand, and maybe sprinkle it with a little salt, or you can bury some cedar chips along with your stones. and be sure to mark the spot, so you don't lose them! Leave them buried for 3 (6,9) days, weeks, or months (the longer, the better, though not so long that you'd forget about them!) you can also get a bowl, and some soil, and place your stones in there. with this method, it's usually best to put it in the sun, or at least out doors.

Sun or Moon- Find a place you know the sun/moon (during the full moon) will touch all day/night (or a good portion of it), and isn't disturbed, like a window sill, or some such. lay your stones out and leave them there all day/night.  If you feel the need, you can repeat the process for three days/nights.  Be sure to bring them in, or simply cover them at dusk/dawn. or you can always do a combination of the two, and leave them out for two nights and a day, or two days and night (or however long you feel they need to be out)

Charging
Usually, if you cleanse a stone in a certain way, you can charge the stone in the same way. simply ask the spirits to lend their energy to the stone instead of asking them to cleanse it. But some other ways to charge a stone would be:

Your own energies - I feel that this is the best way to charge a stone, since it imprints the stone with your own energies. To begin,  Hold you stone in your Projective hand which is generally  your dominant hand.  gather your energy in to your core, which is your solar plexus. Once you feel you've gathered enough energy, visualize it flowing through your hand, and into the stone.  Repeat this as often as you feel necessary.

Formal Consecration - I generally do not feel the need for this.  But, for those that feel a ritual would be more appropriate; cast a circle, and ask the spirits, or perhaps even  the Goddess Herself  to bless and charge the stone(s). 

Programming 
Programming is, simply put,  giving your stone a purpose. Do this only after you're sure the stone is cleansed and charged properly.  To program a stone, hold your stone in your dominant hand.  Clearly picture what you want the stone to do (i.e. soothe a sore back, help you study, bring you good luck, etc) project that picture into the stone.  Do this as many time you feel necessary.  To 'see'  if a stone is programmed fully, do the same thing you do to see if a stone is 'clean'; simply hold the stone and relax and use your inner awareness to get a feel for the stone.  if the reaction is warm, pleasant and clear, you've succeeded in programming the stone.  However, don't be upset if the first time you try to program a stone it doesn't seem work, it just takes a lot of patience, and practice! be sure to pick an appropriate stone for your purpose, if only because it'll make programming that much easier.