The shinobi system in and of itself. It doesn't take a genius to look at the Naruto world and realize how effed up it is. Danzou is the epitome of it, but it's shown throughout the entire series. It's the system that inevitably created or otherwise profoundly impacted and influenced every single villain and problem within the series, from Madara to Orochimaru to Pain to Nemo.

Madara felt as though he was being subjugated by the system he helped create and made inferior to the Senjuu, and thus rebelled, failing in his attempt to take control.

Orochimaru - while clearly an unstable individual from the start and even referred to by Tsunade as such - was also a product of the system, as it was what took him in and turned him into the killing machine he was while simultaneously being the thing to take his parents from him, which is what started him on his path to begin with.

Pain was the inevitable outcome of the system and the perpetual wars and bloodshed it both created and encouraged, forged by the endless pain and loss that it wrought on his village, taking his family and his best friend both away from him while also devastating all his people.

Nemo has manipulated the system to achieve his goals, and could be considered a manifestation of it since he's apparently had a heavy hand in directing it in some form or another, or is otherwise incredibly close to it.