Quartz
In a case of 'rose by any other name', a whole slew of semi-precious gemstones actually fall under a single category: quartz.
Chemically speaking, quartz is made up of a lattice consisting SiO2. One perfect quartz crystal is actually one singular giant lattice (otherwise known as a macromolecule in chemistry).
Many gemstones are actually quartz crystals coloured by impurities, the most important agents being metallic impurities. Colour aside, geologic forces also play an important part in shaping the structure of the crystal lattice.
A non-exhaustive list of such stones include:
Amethyst
Chalcedony
Citrine
Agate
Rose quartz
Jasper
Carnelian
Aventurine
Tiger's eye
This is by no means an academically sound article on quartz nor should it be treated as such. The information cited here was referenced from Wikipedia at:
http://en.wikipedia.org/wiki/Quartz