Very rarely, when a certain creature is slain, the lost life force coalesces into a tiny black orb. Some magickal devices are said to draw on this energy.
Official Strategy Guide
Every third enemy slain (every enemy in the Zodiac versions) will drop a Black Orb that must be interacted with to pick up before it flies away after several seconds. In the First Ascent the player needs to collect three orbs to place on each pedestal on the sides of the waterfall in the middle, and the seal on the locked door will fade. Once the player completes the events at Pharos at Ridorana, the creatures in the First Ascent stop dropping Black Orbs. It may a good idea, then, to pick up as many as possible since they are required later for Subterra, and the enemies there are at a much higher level.
In Subterra, Black Orbs that fly off will combine into a Massive Black Orb in a random spawn point within the same floor containing all the ignored Black Orbs, their number multiplied by three. It is possible to collect very large numbers of orbs in this way, but because Black Orbs are loot, the player can never carry more than 99 at one time. The Black Orbs are used to light Pedestals of Night and the number of orbs required is always a multiple of three.
To quickly light a pedestal without wasting any orbs, the player should add orbs one at a time until a faint light remains above the pedestal to signify one third of the required amount of orbs has been placed. The player can add the last two thirds quickly by taking note of how many orbs have been placed up to that point, and adding twice that many more.
The amount of Black Orbs required on each Pedestal of Night: