Hi Rusty, I'm studying gemmology (big exam at end of June--if I pass I will be a gemmologist), so hopefully I can answer your question.
A gemstone is quite often described as a "stone" or a "crystal".
"Stone" is really just a general term for any inorganic substance that comes out of the earth.
"Crystal" however, should only be used in the case where a mineral has formed a definite external shape, e.g. prism, octahedron. I am not sure how much detail you would like and I don't want to bore or confuse you, so I'll be as basic as possible and if you need more info, let me know.
Some stones are rocks ( an aggregate of several minerals, many different mineral grains which are fused cemented, or bound together) some stones are minerals (consisting solely of inorganic elements, or elemental compounds)
Some examples of rocks are: unakite, marble, sandstone, limestone, lapis lazuli.
All solid matter is composed of material which is either crystalline or non-crystalline, or a mixture of these two states.
In a non-crystalline substance, the atoms and molecules are positioned randomly throughout the material, not aligned in any special order or pattern----because of this---a non-crystalline material can never develop any naturally occurring characteristic shape-----some non-crystalline substances are: glass, amber (organic origin), jet
Majority of minerals are completely crystalline substances whose atoms and molecules are arranged in an ordered and symmetrical three-dimensional pattern or lattice. In most cases this underlying symmetrical crystal structure makes itself visible in the external shape of the mineral specimen----then you would have a crystal-----e.g. quartz prism.
But there are also a few minerals which although they are crystalline do not form an identifiable external profile---these minerals are called "massive" e.g. rose quartz is a massive crystalline mineral, does not usually occur in the characteristic shape of a quartz crystal ( although rarely it is found as a crystal), other examples of massive forms are jadeite and nephrite (polycrystalline), and agate and chrysoprase (microcrystalline.
I hope that this all makes sense. The term crystal is often used to refer to all minerals (crystalline substances), and technically I suppose this is not wrong since they are crystalline substances (made up of tiny crystals). I just think that it takes away from the fact that certain stones form amazing crystals. Amazing that the earth produces these geometric forms from the basic elements.
Hope this helps and doesn't confuse you more, don't mean to be a know-it-all, I'm just so interested in this, Ruby