Positive energy damage results from positive energy, which is normally thought of as life force. From this perspective, positive energy should only damage undead, but it can in fact damage any creature.
This damage type is rare in many modules, as are ways to gain resistance or immunity to it. Positive, magical, and divine damage are the three damage types for which there is no protection via spells, and items granting positive damage protection tend to be rare. Positive energy damage is the only damage type not inflicted by non-epic spells (aside from healing spells used against undead), which alone makes positive damage (typically) the rarest of the damage types.
The epic spell that deals positive energy damage is greater ruin.