The special systems or modules are modules that can be used once in a while, but have a powerful effect. When used they enter into a "cooldown" time, which can be achieved in two ways; for example, that it totally discharges its energy and must wait to recharge at 100% to be used again; or it could overheat and have to wait for it to cooldown.
These systems should be similar to the FTL module in that they should cover the entire ship and have a radius of action.
Some examples could be:
*Short Range Warp / Blink: Uses all its stored energy to move the ship to the target location.
*Cloacking device: Uses all its stored energy to make the ship invisible for a few seconds.
*Energy Burst: This system would use all its stored energy to recharge all the other systems that are in range until its energy is exhausted.
*Time Acceleration: This system would use all its stored energy to make the time go slower for the whole ship (for the outside observer it will appear that the ship and its crew moves faster).
*Engines burst: Uses all its stored energy to make engines to work twice as fast as normal.
*Electromagnetic Pulse: Uses all its stored energy to discharge a powerfull electromagentic pulse to deplete enemy's energy systems.