Terrorism is not some new social disease, it has been around a long time. One rule: these have to be non-governmental organizations. Governments are far more effective at infliction terror on their citizens than NGOs. If I allowed governments then this list would be the SS, Cheka, and the Tonton Macoute.
Night of the Long Knives, Hitler had his SA leadership arrested and executed.
Ku Klux Klan
lynching. Acts that could get a man lynched included looking at a white woman, registering to vote, and not stepping into the gutter when a white man passed on the sidewalk. The KKK still exists today and work underground with neo-Nazis and Christian Identity fanatics. Membership peaked in the 1920's at over five million.
Ribbonmen and the Orange Order
The Catholic defenders evolved into organizations like the Molly Maguires and the Irish Republican Army. The Orange Order gave birth to the Ulster Volunteer Force. The Troubles they caused killed thousands.
Palestine Liberation Organization