Gems can refer to either valuables that are found throughout a wide range of monster and boss loots, as well as gems used in the Gem Atelier.
Common examples of valuables:
But is also commonly including other types of valuables for example:
Finally, it can also refer to the gems used in the Wheel of Destiny through the Gem Atelier:
Greater Mystic Gem, 
Mystic Gem, and 
Lesser Mystic Gem, for druids
Greater Sage Gem, 
Sage Gem, and 
Lesser Sage Gem, for sorcerers
Greater Marksman Gem, 
Marksman Gem, and 
Lesser Marksman Gem, for paladins
Greater Guardian Gem, 
Guardian Gem, and 
Lesser Guardian Gem, for knights
Greater Spiritualist Gem, 
Spiritualist Gem, and 
Lesser Spiritualist Gem, for monks
