Killing an enemy's supply lines is a fundamental tactic that can win the battle for you every time. In addition, you should target Command Ship Support Modules to deny them additional ships. Make good use of 3D space - Don't get into the rut of attacking on a single plane. Group your ships and attack from several vectors at once. Focus fire - Pick the most essential enemy ships and focus the fire of your strike force on them.
Sphere formation centered around an enemy target can be extremely deadly.
Once a target is destroyed, pick another and repeat. Don't neglect defense - Be sure that your crucial assets are well protected. Keep Carriers and your Command Ship out of the battle, and quickly repair any damaged systems. Use Sentinels to set up force fields around these ships as well. Use Sphere formation for defense, or Wall, X, or Claw formation if you're making an offensive strike.