The killswitch is a feature integrated into augmented individuals by Majestic-12 and the Illuminati. It is primarily used as a means to swiftly terminate compromised individuals, particularly renegades.
In Deus Ex, it is revealed that a killswitch was added to Paul and JC Denton when they received their nano-augmentations. Once this killswitch has been activated, it takes about 24 hours for the person to die. The nano-aug killswitch works by programming the nanites in the targets body to replicate exponentially. It is subtly revealed throughout the story of Deus Ex that both Paul and JC have the Gray Death, and ultimately that their nano-augmentations are the Gray Death. As such it is clear that their killswitches amount to making them suffer the same symptoms as any victim of the disease. Paul describes these symptoms as "not worse than a bad cold". This suggests that it is not quite as severe as suffering from the Gray Death itself.
Mechanically augmented agents of UNATCO have a similar killswitch; however theirs is activited by a spoken phrase, called a 'killphrase'. Upon utterance of this phrase, the target self destructs almost instantly. One variant of this type of killswitch appears in the Deus Ex: Human Revolution comic series. It is known as a Dragon-Fire implant and it kills the subject by releasing acid into the subjects's bloodstream.
Physiopharmaceutically augmented agents working for Majestic-12 have what is called a 'self-termination mechanism'. This is essentially a killswitch that activates automatically if an agent is mortally wounded. It has the effect of destroying the agents body (thus removing any evidence of the agent) through an explosion that will also damage nearby hostiles.
In Deus Ex: Human Revolution, the Illuminati seek to replace the biochip of every mechanically augmented person with one of their own construction. This new biochip would allow them to shut off any and all augmentations within a person, effectively making it a form of killswitch. During the game, this 'killswitch' is used to turn augmented people with the new biochip insane. It is unclear if the killswitch can be used to terminate augmented people; although it is apparent that at the change of a signal, the function of the Illuminati's biochip can change aswell.