Gems can be slotted into weapons with the appropriate slots.
They currently are only cosmetic.
It is planned in the future that they will give bonuses. Specifics yet unknown.
There are 3 shapes and 3 colors currently in the game. Red, Blue and Green 9 different gems in total.
Green Gem 2
Green Gem 3
Blue Gem 1
Blue Gem 2
Blue Gem 3
Red Gem 1
Red Gem 2
Red Gem 3