As much research as I've done over the years, there are some sources that elude me, or those I've simply forgotten in the glut of other information I've gathered. These are gems which I know to exist, having them in my collection or knowing people who do, but do not know from whence they came.
a tiny nugget of animite
a small silver-laced quartz
The following is, to my knowledge, the only altered gem in game.
a pale blue pearl delicately engraved with a serene dolphin leaping from a balmy sea
The tiny dolphin has been painstakingly rendered to follow the curve of the pearl as it leaps joyfully from a cresting wave.