Certification of gemstones does not indicate the quality of gemstone. Certificate only certifies if the said gemstone is real or fake; and in some cases treated or non-treated.
Quality of gemstone depends on color, clarity, cut and carat (the same 4C’s used for diamonds). Thus, better the quality, better the price and vice-versa.
COLOR: For different gemstone, different shades of color will have varied price. For example: Light blue sapphire will be cheaper while medium-dark blue sapphire will be higher in terms of price but very-dark blue sapphire price would again be cheaper. So, overall, intensity of color in gemstone many not always increase the price.
CLARITY: For different gemstone, different clarity (purity/inclusion) of gemstone will have varied price. For example: amber with an inclusion of lizard/ant will have higher price than a clean amber gemstone. But, generally, the clearer the gemstone the higher the price. (Note: A clean gemstone can also indicate a fake gemstone when price is very low.)
CUT: A better cut gemstone will always have a higher price.
CARAT: The bigger the size of gemstone, the greater the price.
Determining the quality and price of gemstone (color, clarity and cut) is not an easy task for a novice user. An experienced trader can only calculate it based on his/her experience.
Also, you can check out my post on how to identify blue sapphire for more information.