"By your leave" is a Colonial expression roughly analogous to the "by your command" used by the Cylons.
It is used at least twice in the Original Series. Once, by a Council Security officer seeking permission to exit the sendoff arranged for Captain Apollo by the pilots of [[Blue Squadron] (TOS)|Blue Squadron]] (Lost Planet of the Gods, Part I), and on another occasion, Boomer uses it to close a video communication with Commander Adama.