Allows for modules to perform above their standard values, for a limited time and for a cost and potential module and intregrity damage. You could also reduce your module power to reduce your radar signature, similar to cold running, but more on a sliding scale than a binary on/off, to reduce fuel consumption, or as a balance for other "overcharges".
Ingame Reasoning: The performance of the modules is standardized within safety limits and allow for a low-wear operation of the equipment. By closely monitoring their output values, it should be possible to slightly improve their performance. The consequences should increase faster than the gain, so slight tuning is relatively painless, but gaining boni should require permanent supervision and fast reactions.
Thrusters could be overcharged, similar to what the Planetary Approach Suite does, to allow higher performance, but with increased heat generation, power and fuel consumption. It would also come at the cost of other thrusters, so if you want more speed, you lose maneuverability, if you want more yaw, you lose pitch and speed, and so on. Should consume ENG-Energy. Requires good communication with the pilot.
Boost could also be modified, faster with higher ENG-Drain, or slower with lesser ENG-Drain, maybe even able to be maintained until the capacitator is empty, with fast rising heat. Crew member could allow the Pilot to "perma"-boost until the gauges get into the read, then put them on extended cooldown and repairs.
Weapons could fire (all but beams) and reload (if applicable) faster, deal more power per shot (pulse, burst, plasmas) or time (beams). This would increase ammo consumption, more WEP-Energy, heat generation, damage the modules and use more power from the generator.
Scanner could make a ping like an active sonar, improving its range for a moment, but also showing you on everyone's radar for an even greater range. should use quite a lot of SYS-Energy. In addition, overcharging it might increase its range all the time, at the cost of more heat, more power consumption, significantly higher radar signature and damage to the module over time.
Shields could be set to recharge faster (SYS-Drain, generating more heat, straining the generator), recharge while under fire (damaging the shield reactor if the shield is damaged while recharging), go above their max (permanently using SYS-Energy, generating more heat, straining the generator), allow a reinitialisation even if it is not 50% charged yet (with damage to reactor, heat spike, SYS-Drain)
FSD could allow a blind jump, where you jump before all the safety calculations, that normally guarantee your safe journey, are turned off. This would allow jumping while mass locked, but destroying the FSD in the process (requiring a reboot) to limp back to civilisation afterwards. Also, destination might not be safe at all.