By your command the affirmative response given by Cylons to an order. It is roughly analogous to the Colonial "So say we all", but probably not with the same religious overtones.
It's speculated that it could be an artifact of the Cylons' original programming; that when the Cylons were still working for the humans, they were programmed to say "By your command" as a catch-all affirmative reply to their human masters' orders, and that after they rebelled it just stuck around in their lexicon. When Number Six is told that the Cylons must hunt down Galactica and the rag-tag fleet, she responds "By your command". (Mini-Series)