Base damage indicates the damage a weapon deals on its own. The amount and type of damage dealt depend upon the source of the damage. All physical damage that is made in an attack will be treated as using the same damage type as the base damage.
Unarmed attacks deal bludgeoning damage based on the creature's size (d2 for small and tiny creatures, d3 for medium, large, huge creatures). The monk class overrides the unarmed damage with an improved unarmed progression. Gloves are used for adding magical benefits to unarmed attacks.
Weapons equipped in the right and left hand slots deal the damage and damage type assigned for that weapon in baseitems.2da, while weapons equipped in natural weapon slots (typically creature weapons) use the damage type from baseitems.2da, but have their damage defined by the monster damage item property.
The damage types used for base damage can be expanded to include other physical damage types by the extra melee damage and extra ranged damage item properties. When a weapon has multiple damage types, all physical damage dealt by attacks with it will affect its target using the higher of armor class bonuses/penalties per armor class type (with the exception of dodge AC which stacks with itself), and the lower of the damage immunity and damage resistance.
When stacking damage bonuses, the base damage will always stack with damage bonuses and feats regardless of their damage type. A +5 enhancement longsword will deal 1d8 base damage + 5 bonus damage even though the enhancement bonus always uses the same damage type as the base damage. However, a +5 longsword with +5 slashing damage, will still deal 1d8 base damage + 5 bonus damage, because the enhancement bonus is the same damage type as the damage bonus. When the base damage covers multiple physical damage types, the enhancement bonus will only use one of these to determine whether it stacks with damage bonuses. Piercing-slashing weapons will have the enhancement bonus conflicting with slashing damage bonuses, while bludgeoning-piercing weapons will have the enhancement bonus conflicting with piercing damage bonuses.