Custom Minerals are a great way to get powerful tools and armor with enchantments and stats that can't be found on vanilla items. They can be enchanted like normal and are also textured with unique colors. To trade your gems, talk to the Miner at spawn and trade them in for any tool of your liking.
Miner Shop at spawn
How to Obtain Custom Minerals
Towny Capture Sites can sometimes give minerals
Towny Resource Surveying has a chance to give your town daily minerals.