I think that off-color gems would add some interesting elements to the game. Each variety of existing gem could have one or more off-color variety that has a chance of spawning in place of the regular gem variety when they are generated into the world. Off-color gems would be a tint or shade of a different existing gem. Off colored gem tools could offer dual or hybrid effects between their gem type and gem color As an example, Padparadscha Sapphires are pink, so as an off-color variant of sapphires, they would have properties of sapphires and rubies. It would also add more variety in gem-based builds, which is an awesome bonus.
Inversely, off color gems could instead replace most gems on a planet, offering various minor alterations to the stats of a finished product, with “perfect” gems being rarer and offering a considerable bonus over lesser varients.