Historically gems have been used for all kinds of things. They aren't just bits of glass and they do have definite properties. Quartz for example has a positive electric charge. It is used in countless electronics. You may remember the old 17 Jєωel watch that had tiny rubies and other gemstones in the works.
Gems and crystals are beautiful and as all creatures of God, can be used for good or bad purposes. They can be used in witchcraft but they are also used in bishops rings and wedding rings.
I am personally not going to allow new agers to have all of the good things. They have already taken the perfectly good word "gαy" and most of the gorgeous places in the world to live. So if I want to hang a beautiful crystal to lift my spirits or cast fantastic colours on the wall when the sun hits it just right, I will do it. For Heaven's sake, these things were given to us to use. As long as we don't attribute supernatural or preternatural powers to them or use them for evil purposes, then we don't have to worry.
As far as using a stone for healing, who knows? We use fungus and call it medicine, what is really the difference between using a rock and using a plant for medicine? Quartz, as I mentioned, has an electric charge. French green clay also has an electric charge and it is used for all kinds of wounds and digestive troubles, because having a negative charge, it attracts to itself pathogens and parasites which have a positive charge and then they are collected by the clay and eliminated from the body. We really don't know all that much about the natural world ultimately. We are finding new things out every day.
St Albert the Great wrote a study on gemstones called De Mineralibus and he believed they had definite natural properties. St. Hildegard von Bingen also believed that gemstones had their own healing properties. She wrote "Physica" which contained what she knew of gems. She was renowned for her healing abilities with herbs, stones, metals and whatever God provided in nature.
http://www.minrec.org/libdetail.asp?id=20http://www.scribd.com/doc/108541883/Stones-and-Metals-Physica-by-St-HildegardWe shouldn't throw out old wisdom just because modern science, which is more witchcraft in the way it is used (to prevent pregnancy, to kill unborn babies, to create life outside of natural conception, to create chimeras, to delete and add genes in an attempt to create supermen, to create destructive weapons and weather) than anything in medieval times, has deemed it worthless. Good people in ages past knew how to use God's gifts. To me it almost is a sign of superstition to be afraid to use gemstones because one is afraid of them. That is certainly attributing power to them they do not have.
St. Eligius is the patron of Jєωelers and St. Albert the Great patron of natural science, pray for us.