The Inquisition, in all its aberrations, may lead the lot. Christian and Muslim hatred of the Jews is right up there too. Nazis of all descriptions, of course, starting with Hitler's Germany. The Ku Klux Klan are evil, as are the other White Supremacist groups. Then you have religious terrorist groups like the IRA and Al Qaeda. Lots of others that I'll be interested to read about in other answers. I was almost tempted to add the Tea Party, but I haven't learned enough about them yet to do so.
The Nazi party in Germany during the mid-1940's was a huge one. 12 million people were killed in the Holocaust--Jews, homosexuals, the mentally and physically disabled, Communists, and anyone that challenged the Nazis, and anyone that was considered "undesirable" by Hitler. He wanted a pure German race.
The KKK (Ku Klux Klan) is another big "hate group." They couldn't stand the emancipation of African Americans from slavery. They burned buildings and killed people to show their power. They wore white robes and pointy white masks to conceal their identity, and white because, well, they were white supremacists.
And there is Al-Qaeda. They are an extremist group of mainly Muslims that have a prejudice against Americans. Osama bin Laden was the leader of Al-Qaeda until the Navy SEALs in 2011 killed him. Al-Qaeda is blamed for the 9|11 attack at the World Trade Center in 2001. Four planes were taken over by members of Al-Qaeda. Two ran into the Twin Towers in New York, NY. One was recaptured and crashed in Philadelphia. The other was flown into the Pentagon.
Over the years, there have been many "hate groups" throughout the world. Most of this hatred is stemmed from prejudice.