Penix 2.0 is an operating system that Ghost claims to have programmed in his spare time, where he would release a virus with his hacker skills called "digital AIDS" to certain people listening to his broadcast.
The system itself
Penix 2.0 is also able to track the IP address of every computer currently listening to his broadcast. Ghost has stated that only select members of the Capitalist Army will have access to Penix 2.0. It's been speculated to be either an derivative or variation of the operating system Linux, especially since both systems have similar names.
"Digital AIDS" is supposedly able to infect any computer connected and then make it an infected computer and will turn the computers into "coasters", presumably because they'd be unable to function as anything but a place to put your drink.
Despite the fact that Ghost refers to Penix 2.0 as an "operating system", the operations he allegedly uses it to perform generally imply that it is more like a standard computer application. However, in a PalTalk session, Ghost revealed that Penix 2.0 has a built-in web browser called "Balls Explorer", whose icon is two spherical balls. The user interface of this browser is apparently all contained in a single toolbar which he dubbed the "Shaft Toolbar".
The first known instance of Penix 2.0 was on Episode 96, as a caller inadvertently brought up the OS. He was shocked at how it leaked out to the public.
On episode 226, Ghost claimed that the system had already been put to use doxing several bronies. Ghost stated that the dox uncovered by the program revealed that many of the bronies claiming to be teenagers were really adults and implied that they were all pedophiles. The operating system was apparently activated by Ghost on May 16, 2012, despite his claim that he had used it already on the episode the day prior.
Penix 2.0 was possibly put to use in the Twitter hacking and doxing incidents, as someone claiming to be Ghost had dropped names of individuals who have either been annoying him, or had bad relations with him in the past on his Twitter. This became evident in late September 2013, when GNAA members had names, locations, and phone numbers all released by someone who was pretending to be Ghost. Many of these doxes are confirmed to be incorrect, though.
Ghost continues to occasionally reference Penix 2.0 when threatening reprisal against trolls, such as during Saturday Night Show Episode 3, when he threatened to use the software to dox the creator of a splice of Ghost saying "I freaking love child pornography!"
During The Ghost Show Episode 21, Ghost stated that Penix had been upgraded to Penix 3.0. What differences this has from Penix 2.0 is yet unknown.