A holy weapon is imbued with holy power. This power makes the weapon good-aligned and thus bypasses the corresponding damage reduction. It deals an extra 2d6 points of damage against all of evil alignment.
This the relevant text in the entry on holy weapons in the SRD. Holy weapons could plausibly deal:
- Holy damage
- The same type of damage as the weapon
- Divine damage*
- Untyped damage
* Consecrate spell (BoED/CD) gives spells the good descriptor and makes half the damage divine. A spell in the SRD that deals divine damage is flame strike.