The phrase first came to public attention in George Lucas's Star Wars trilogy. It is the view espoused by Darth Vader, Emperor Palpatine, et al.
The term itself is quite difficult to define. In the movie, it refers to actions one might take that are the result of fear, uncertainty, doubt, or other negative feelings. These are "inevitably" self destructive.
In popular culture, "the dark side" has come to refer to the seamier aspect of something. For example, The Dark Side of Psychiatry or The Dark Side of the All-American Meal.