You can upgrade 3 of the same type of gems to get 1 gem of a higher quality.
upgrade chipped gems
upgrade flawed gems
upgrade normal gems
upgrade flawless gems
These runes don't require a gem to upgrade.
These runes require a gem and 3 runes to upgrade.
These runes require a gem and 2 runes to upgrade.
Secret Cow Level
Token of Absolution
Consult the dedicated crafting page for all crafting recipes.