Chakra Guide
As quoted from Bestcrystals.com:
There are 7 major Chakra centers of the physical body, where vital energy flows and intersects. Through our Chakras, we transmit and receive physical, emotional, and spiritual energy. The chakras are manifested in one's physical state. The ideal is to have all chakra centers clear, balanced, and vitalized for optimal well-being. The chakra system goes back to ancient eastern masters. Each chakra is associated with a particular area of the body and a color of the spectrum. Stones are used at chakra centers for clearing, revitalizing, and healing. Crystal wands are utilized to open the chakras. Generally, the selection of stones correspond with the associated color of the chakra.
The stones listed are links - just click to go diretly to that stone page
1st Chakra
Base, Root
Located at the base of the spine
colors: red, black
energy focus: Stability, grounding, physical energy, will, security.
stones:
Hematite
Black Obsidian
Black Tourmaline
Red Zincite
Garnet
Spinel
Smoky Quartz
Aegerine
Jet
Moqui Marbles
Zircon
2nd Chakra
Sacral
Located below the navel
colors: orange, blue-green
energy focus: Creativity, healing, sexuality and reproduction, desire, emotion, intuition.
stones:
Orange Calcite
Vanadinite
Carnelian 
Blue-green Turquoise
Blue-green Fluorite
Copper
Imperial Topaz
3rd Chakra
Solar Plexus
Located at solar plexus, below breast bone
color: yellow
energy focus: Intellect, ambition, personal power, protective.
stones:
Citrine
Amber
Yellow Jasper
Golden Calcite
Yellow Apatite
Gold Tigereye
4th Chakra
Heart
Located in the center of the chest
colors: pink, green
energy focus: Love, compassion, universal consciousness, emotional balance.
stones:
Rose Quartz
Cobaltian Calcite
Pink Danburite
Lepidolite
Rosasite
Vesuvianite
Pink/Rubellite Tourmaline
Watermelon Tourmaline
Green Aventurine
Malachite
Jade
5th Chakra
Throat
Located at the neck above collar bone
color: blue
energy focus: Communication center, expression, divine guidance.
stones:
Sodalite
Blue Calcite
Blue Kyanite
Chrysocolla
Celestite
Blue Chalcedony
Angelite
Blue Turquoise
Amazonite
Aquamarine
6th Chakra
Third Eye
Location centered above eyebrows, at medulla
color: indigo
energy focus: Spiritual awareness, psychic power, intuition, light.
stones:
Lapis Lazuli
Azurite
Tanzanite
7th Chakra
Crown
Located at the top of the head
color: violet, golden-white
energy focus: Enlightenment, cosmic consciousness, energy, perfection.
stones:
Amethyst
Apophyllite
Herkimer Diamond
Quartz Crystal
White Hemimorphite
White Calcite
WhiteTopaz
White Danburite
White Howlite
Selenite
Chakra qualities of the stones
As quoted from Bestcrystals.com:
As you become familiar with stones, meditation, healing work, and the energies within and around you, you will begin to incorporate your awareness into different aspects of your life and consciousness. Studying and working with the chakra system will help you become aware of the powerful life force energy that exists within our bodies, minds, our environment, and ultimately the physical and divine universe. Your body is indeed your temple!
Below is a brief listing of stones and their use with the chakra system to get you started.
Amethyst
 Opens and activates crown chakra
Celestite
 Aids in clearing and perfecting chakras
Citrine
Balances energy and aligns chakras with ethereal plane 
Activates and opens navel and solar plexus chakras 
Energizes the root chakra 
Stimulates crown chakra
Amber
 Opens and cleanses 3rd chakra
Copal
 Activates crown chakra
Green Aventurine
 Activates, clears, protects heart chakra
Bloodstone
 Awakens and balances 1st through 4th chakras 
Centering and grounding for the heart chakra
Clear, white Calcite
 Stimulates energy of all chakras, excellent at the crown chakra
Carnelian Agate
Use with the 1st through 4th chakras 
Physical energy, creativity, compassion
Chrysoprase
Aligns chakras 
Activates heart chakra
Herkimer Diamond
 Acivates crown chakra
Green Flourite
 Good for cleansing, renewing chakras
Garnet
 Stimulates base chakra 
Removes negative energy from chakras, promotes physical healing
Hematite
 Good for treating and closing the root chakra
Pink Kunzite
Activates heart chakra 
Aligns and balances the chakras
Kyanite
Aligns all chakras automatically 
Can be used to open chakras
Lapis Lazuli
 Activates and clears throat and third eye chakras
Malachite
 Stimulates heart and throat chakras
Moldavite
 Use at the throat, third eye, and crown chakras
Moonstone
 Cleanses negativity from chakras
Black Obsisian
 Grounding, good for the Root chakra
Tigereye
 Promotes intuition at the solar plexus chakra 
Enhances psychic ability at the third eye chakra
Turquoise
 Elevates and attunes all chakras 
Facilitates communication skills at the throat chakra
Black Tourmaline
 Stabilzes root chakra, dispels negativity, good for the lower back
Green Tourmaline
 Heart Chakra
Deep Pink Tourmaline
 Stimulates base chakra and connection to heart chakra
Watermelon Tourmaline
 Superior activation of the heart chakra
Rose Quartz
 Loving energy to the heart chakra 
Balances energies of all chakras
Quartz Crystal
Opens all chakras 
Activates crown chakra, clarity of conscoiusness
Balances and heals emotional wounds at the heart chakra
Smoky Quartz
 Root chakra
 
 
 
             
         
                                                 
                                                         
                                                         
                                                         
                                                         
                                                 
                                                         
                                                         
                                                 
                                                         
                                                         
                                                 
                                                         
                                                         
                                                 
                                                         
                                                         
                                                 
                                                         
                                                         
                                                 
                                                        