I saw this post and figured I'd add my lingo into the mix ^_^;
"Running Silently" - Keep the ship fully repaired, buffed, chemsprayed, and on the look out for targets, but don't shoot them.
"Battle Stations" - Everyone needs to get where they should be during a combat encounter, cause there's about to be one in the next 30 seconds.
"Buff-run" - Buff engineers buff the entire ship ASAP
"No ____" - The enemy shouldn't have whatever is in that blank within the next 10 seconds, usually a component (i.e. "No Lumberjack" = "Take out the Lumberjack ASAP").
"Sharp-shoot" - Snipe out any and all enemy components at close range.
"I need ___!"/"I need ___ yesterday!" - Fix the component...Now.
"Where's my ____?!" - Usually translates into "Why isn't that particular gun firing?"
My other commands are a bit more "generic" and have been included in the previous posts, like "kerosene/moonshining", "butt-ram", "sitting/goomba-stomp", "uppercut", etc.
EDIT: Thought of one more
"I'm putting you in time-out!" - Usually said to a 2nd Gunner, or a Gunner that isn't listening. I turn the ship around entirely so they don't have gun-archs, and stay like that until they do as they're told, even at the cost of showing our backs to the enemy >_>;
