Crystal is a resource that, along with metal, is common and used in most buildings and ships. This resource is prized as it is used to research some high level techs. It is also used in some high tier ships and ship upgrades.
Fuel is a rare resource that can be acquired easier on planets far away from the sun. This resource is made from refined hydrogen and is used to power ships and defenses. This is the primary resource used in techs.
All of these resources can be gained from their respective mines. Or they can be stolen from other people.