There could be several kinds of gemstones, each native to a different type of rock and dropping from that rock very rarely when a square is mined. When quarrying mountains is implemented, there could be several types embedded exclusively in those. They could also appear extremely rarely as visible curios on mountains and in riverbeds.
Each individual gem would be in its rough state when mined or gathered, and require a Gemcutting skill (would need Jewelry as a prerequisite), and likely a dedicated workbench, for refinement. The quality of the workbench and value of the player's relevant skills would determine the quality of the refined gem, using the quality of the rough gem as a basis.
I feel like this would add a lot of variety to the jewelry and customization of the game. Maybe in addition to the pre-set jewelry recipes we have, there could be recipes for generic metal rings, bracelets, crowns, arm bands, etc.- upon which precious stones could be mounted according to how many available slots that particular kind of item had open for gems. Each type of gem might have a quality-modified boost to a certain stat, thereby allowing players to customize their equipment bonuses through adornment. Also, gems on metal weapons.