The great powers are what Count Iblis claims destroyed his ship.
When asked about them, Iblis is initially evasive, other than to scoff at the possibility of them being Cylons. When pressed by Adama, Iblis reveals that "there are greater and more infinitely dangerous powers in the universe than your Cylons and all their allies combined."
It is unknown whether the powers were in fact the Beings of Light or other forces (TOS: "War of the Gods, Part I").