A damage bonus on a weapon increases the amount of damage inflicted in combat. A weapon can have multiple damage bonuses; those of different damage types stack, while those of the same type do not. For the purposes of stacking, an enhancement bonus is considered a damage bonus of the weapon's base damage type. After stacking is determined, all physical damage bonuses are converted to the weapon's base damage type.
A damage bonus is distinct from an on-hit property that inflicts damage. Such properties (such as from flame weapon) are resolved independently, before the damage from the weapon itself is calculated.
There is a distinction between a damage bonus (on a weapon) and a damage increase effect (on a creature). Some spells and abilities (e.g. deafening clang) provide a damage bonus that remains with the targeted weapon (so swapping weapons means that the bonus is no longer used). Other spells and abilities (e.g. prayer) provide a damage increase to a creature that remains in effect regardless of the weapon being used. Distinguishing these two cases can be confusing at times, since both can be called "bonus damage", and many spells that target weapons allow the targeting of a creature with an implied targeting of that creature's main-hand weapon (or creature weapon).