Buying a gemstone is a very different experience than buying a diamond. The major factors that affect the price for colored gemstones are: Cut, Color, Clarity, Carat + Country of Origin.
Carat
Gemstones all have different densities, and typically have more mass per unit volume than diamonds. Though a gemstone may look the same size as a diamond, the gemstone will usually be more in weight. (i.e.: 1-carat ruby will look smaller than a 1-carat diamond.)
Color
Gemstones are judged based on the translucency, tone, and uniformity of color. A gemstone should never be too light or dark.
Cut
The quality of the cutting, symmetry, and polish is the most important criteria that affect the value and the beauty of the gemstone.
Clarity
This refers to the presence or lack of inclusions that affect a stone's appearance and overall durability. The clarity for gemstones are graded on the visibility of the inclusions to the naked eye. (Unlike diamonds, that are graded under 20x magnification.) Some gemstones such as emeralds are graded by their own standards.
Country of Origin
The same gemstone may be found in different regions, but the chemical composition of the soil ultimately determines the gemstone's color, clarity, and quality. For example, a Ruby may be found in various countries of Asia but the most revered color is pigeon blood and only comes from Myanmar, Ceylon blue is the most desirable color for sapphires and are only found in Sri Lanka, and the emerald green colored emeralds only comes from Columbia. Many gemstone's supplies are finite and some are so rare that they are considered to be only a one generation stone.
