Wooden Stakes are needed to kill vampires permanently, because they all become mist when they are defeated. You don't need them for every vampire you come across, only in quests related to vampires where they retreat to a coffin. This item appears in Baldur's Gate II: Shadows of Amn and Baldur's Gate II: Enhanced Edition.
They can be bought at many temples, like the temples of Helm and Lathander.
In-game description
| “ | A sharpened, wooden stake that is marked with the holy symbols of Selune. Legend has it that staking a vampire will put them permanently to rest... although likely the vampire would have to be immobile (at rest) in order to do so properly. | ” |