Damage is a decrease in hit points, an ability score, or other aspects of a character caused by an injury, illness, or magical effect. The two main categories of damage are lethal damage and ability damage.
In addition, wherever it is relevant, the type of damage an attack deals is specified, since natural abilities, magic items, or spell effects may grant immunity to certain types of damage. Damage types include weapon damage (subdivided into bludgeoning, slashing, piercing), and magical damage (positive, negative, acid, cold, electricity, fire, sonic, magical, and divine).
Modifiers to melee damage rolls apply to both subcategories of weapon damage (melee and unarmed). Some modifiers apply to both weapon and spell damage, but only if so stated.
Damage points are deducted from whatever character attribute has been harmed -- lethal damage from current hit points, and ability damage from the relevant ability score. Damage heals naturally over time, but can also be negated wholly or partially by curative magic