About 50% of a gemstone's value is related to its color. Color in a colored gemstone is in itself graded by saturation or intensity, tone (how light or dark it is) and hue, or purity of color. Since most stones have at least one modifying color, such as yellow, we grade the modifying colors for rarity and beauty. For instance, a blue sapphire with a slight yellow or greenish tint is considerably less rare and less expensive than one modified with violet. In some cases it helps determine where the stone was mined, which also might effect value. You do not need to understand this perfectly to buy a fine gemstone. Choose a color that you like and prefer if possible.
The color grading system most commonly used today grades clarity with the same terminology as diamonds. It uses also however a type system that classifies each gemstone by type. A type 1 stone is one that normally comes eye clean such as aquamarine. A type 2 is one that has very slight variations to the eye such as a veil or thumbprint inclusion which you might not be able to focus on but affects the light as it travels through it. A type 3 stone normally comes heavily included such as Emerald. Clarity is relative to the type of stone, as some stones come crystal clear while others are normally silky or cloudy looking.
Cut is graded much more loosely than a diamond, where proportions and symmetry are very tightly graded because of the brilliance that can be achieved. Colored stones are graded within tolerances for shape using outline balance, as well as length and width and depth ratios. The grading will take into consideration bulge, table percentage and girdle thickness. The polish will be described as finish and will take into account the polish surface, the arrangement of the facets as well as their shape and number. The fact is these really are generalized, unless you are grading a top color and or clarity gemstone.
There are some issues not exactly fitting color, cut or clarity that affect price. A good example are stones that are not transparent but rather translucent, which are graded within an entirely different pricing structure. Most cabochon stones for instance are translucent. Another issue is that some stones such as sapphire have zoning or layers of color. When the zoning leaves clear areas when viewed at even an oblique angle to the stone the stones are priced at much less than uniformly colored stones. Gemstones that normally are mined in thin veins such as opal and jade but are stronger or brighter when in a thicker stone are priced significantly higher for the thicker stone.
In the last decade the tendency to include carat weight as if it were a grading issue has dominated the market. The simple point is that most gemstones are sold by carat weight. There are jump points in price for stones usually based on rarity. Each stone is different. Some of the differences are being erased by efforts to standardize grading and pricing. I know that not that long ago a third of a carat ruby was considerably more per carat than a quarter of a carat ruby, while its sister stone sapphire didn't jump in price until it weighed over a half a carat. Price guides within the industry have made their pricing structures closer to a diamonds. This will make for real price differences between dealers (in certain sizes under 1ct) for some time to come. Being aware of this may help you spot a bargain.