[Fishmachine]

I always aim below the waterline, into areas where fuel bunkers are supposed to be. It's the quickest way to sink a ship. With a succesful shot it will break in half and explode. Engine room is always close to the fuel bunker, so it's also natural target.
Also, hitting below waterline causes fastests flooding so it's the best even if you don't hit fuel bunkers.
Hitting cargo can cause some spectacular fires, but no serious damage to the ship. Aiming at the command posts can at least slow down ship, but I see no point if it's in range of accurate fire.