Snake Hibernation
Snakes such as rattlesnakes, garter snakes and copperheads congregate underground, sometimes in large numbers, starting in October, to hibernate and lay their eggs. These underground dens are sometimes referred to as snake pits.
Human Execution
Several historical references exist that describe people executed in snake pits. In Viking legend, Ragnar Lodrok was captured by King Ella of Northumbria in the mid 800s and cast into a snake pit. In these stories, people gathered snakes, put them into a pit and deprived them of food. Then human victims were thrown into the pit and left to die. The efficacy of this system is questionable, as even venomous snakes tend to be shy.
Mental Health Facilities
Mental health institutions were called snake pits because of the thousands of mentally ill patients given little or no treatment while housed in overcrowded facilities, like so many snakes in a pit. A 1963 Time magazine article describes one Georgia clinic as a "monstrous snake pit," with 12,000 patients and just 50 doctors, only three of whom were psychiatrists who might have actually been able to treat the residents. The concept of mental health facility as snake pit was popularized in the 1948 move, "The Snake Pit," in which a housewife, losing her grip on reality, checks herself into a state hospital, where she is abused by workers and other patients.
Chaos and Disorder
In a 2010 Time magazine article, Joe Klein refers to the current war in Afghanistan as "the same old Afghan snake pit --- a sapping struggle, largely an Afghan civil war, with no clear end in sight." The term "snake pit" here is used as a metaphor for the chaos and disorder found today in Afghanistan.