Rocks and stones which have formed in accordance with a definite ordered internal structure or geometric lattice are called crystals.
Most crystals were formed over millions of years through shifts in the massive plates that make up the outer layers of the earth. When super hot steam escaped from deep inside the earth, minerals contained in this steam changed their nature through heat and pressure and cooling down, crystallised in fractures and folds in the outer crust of the earth.
There are some exceptions:
Obsidian is a natural glass formed through volcanic activity.
Tektite owes it’s existence to meteorite impact and in parts comes from outer space. Moldavite is a green variety of Tektite only found in Moldavia.
Fossils are organisms of a past geologic age, embedded and preserved in the earth's crust and have their beginnings in the oceans, rivers and forests of ancient times.
Jet is a resinous, hard, black variety of coal that started it's journey as fossilised wood.
Coral, Shells and Pearls are the gems of the sea.
Amber & Copal aka Kauri gum, are fossilised tree resins.