Note that damage against armor is further reduced by up to 85%, depending on the weapon's per-shot damage and the target's armor strength.
High Explosive weapons do 200% damage to armor and 50% damage to shields. They are thus most effective at destroying the armor of targets with shields down. High Explosive damage is used by most missiles, many ballistic weapons and the High Intensity Laser.
Energy damage is equally effective against all targets, doing 100% damage to shields, armor and hull. It is used by almost all energy weapons and the ballistic Mjolnir Cannon. Many energy weapons also have advantages such as being constant damage beam weapons or secondary effects.
Fragmentation weapons do 25% damage to both shields and armor, and are thus ineffective against protected targets. However, they generally have very high DPS and are thus extremely dangerous to thinly armored, unshielded targets such as missiles and fighters, as well as ships which have had their armor stripped away by damage. The Vulcan Cannon, Thumper, Salamander MRM and Stinger-class Proximity Mine do Fragmentation damage.
EMP damage disables weapon & engine components without harming shields or hull. It is mostly found on energy mount weapons that also do energy damage such as the Ion Cannon although the ballistic Hypervelocity Driver and Salamander MRM series of missiles also do EMP damage. The exact mechanics are discussed in the EMP page.