It is sad and along the same lines as pohnpei397, was the expulsion of the Jews from Spain by King Ferdinand and Queen Isabella in 1942. Tens of thousands of Jews were forced to leave. A large portion of them headed to Turkey and the Sultan Bajazet is believed to have welcomed them warmly saying,
How can you call Ferdinand of Aragon a wise king, the same Ferdinand who impoverished his own land and enriched ours? [i]
There have, sadly, been so many examples of prejudice in the history of the world that you should not have much trouble with this.
The most extreme example of prejudice must surely be the Holocaust. Prejudice does not have to be violent like the Holocaust was, but the Holocaust was clearly motivated by prejudice if you use the following definition of prejudice that is seen in the link below:
an antipathy based upon a faulty and inflexible generalization. It may be felt or expressed. It may be directed toward a group as a whole, or toward an individual member of that group.
Another major example of prejudice in the United States has been the attitudes of whites towards blacks over the course of our history. This prejudice was manifested in such things as slavery and the racial segregation of the Jim Crow era.
There are examples of religious prejudice in the world was well. An example of this would be the "Troubles" in Northern Ireland that were motivated at least in part by religion. There have been examples of killings of Christians by Muslims in Iraq that were based on prejudice and the fighting between Shiites and Sunni there are also examples of prejudice.
All of these are famous manifestations of prejudice.