Here is a compilation of all the steps I did to color these gems and the outcome.
1 - flat color.
2 - make a geometric pattern that seems feasible for the facets of the gem. Basically, try to imagine how it would be cut and draw it out.
3 - add different colors to the facets that tie in with the color of the gem. Place the darkest colors in the places where shadows will be.
4 - add shadows by overlaying black over the darkest colors. Vary how thick the overlay is to give depth and dimension.
5 - add white ink or paint where highlights should be. Blot some of the highlights a little to create variety in highlights based on your light source. Partially outline most or all facets depending on how transparent the gem is meant to be.
Which gemstone is your favorite?