Some precious gems would be boring if they were pure. Both emeralds and rubies in their pure form are colorless, yet we know rubies by their deep red color and emeralds by their rich green. Both colors are caused by a small amount of chromium in the gems, and their differing color has to do with the interaction of chromium with certain crystal structures. In other words, the gemstones' colors are not pigments, but are in the light-absorbing powers of their chemical makeup.
Rubies are composed mostly of the mineral corundum, which in its crystallized form consists of aluminum ions each surrounded by six oxygen ions. Emeralds are made of beryl, which contains beryllium, aluminum, silicon and oxygen. Each aluminum ion is surrounded again by six oxygen ions just like in a ruby, but the beryllium and silicon make the mineral very different. Throw a little chromium into the mix and you can tell rubies from emeralds just by color, because the chromium in emeralds absorbs red light and leaves it looking green. Rubies absorb green light, making its chromium look red. This is explained in much more detail at the Conversation, but they still can't explain why people pay so much for these stones.
(Image credit: Vassil)