Funny the things you find out when you start doing research. I always "knew" that the Crusaders killed Muslims in the Holy Lands; it wasn't until this year that I found out that not everyone in the First Crusade worried about reaching their goal before they started killing "infidels". Some impatient Crusaders decided there was no point in going all the way to the Holy Land to kill infidels when there were Jews in Europe. Jews were appealing targets of Christian hostility for several reasons. Theologically, they had originally worshipped the true God but refused to worship Christ; this made them enemies of God and the Church, so they deserved to be treated harshly. Economically, Jews had no prohibition against usury, the lending of money for interest, so they became merchants and bankers to the Christians – meaning that Christians often owed Jews money, which the debtors resented, and killing Jews was a way to cancel the debt; even if there were no debts, the Jews represented a chance for good looting. Politically, Jews had taken the anti-Christian side in the Holy Land since the seventh century, primarily because Islam generally tolerated them as another "people of the Book" (the Old Testament). Popularly, Jews were “other”, foreign in a time when strangers were automatically suspected; because their religious rituals were strange to their neighbors, Jews were often accused of witchcraft, in particular of using Christian blood and killing Christian infants in their ritual.
In 1096, the People's Crusade, the first branch of the Crusade to leave France, made its way into Germany, where the hot-headed among the Crusaders decided to eliminate the Jews before continuing to the Holy Lands. Jews were massacred and temples desecrated in Spier (in spite of being sheltered by a Christian bishop), Worms (where 1000 died), Mainz (where they were protected at first by the archbishop, who later fled; 900+ died), and Wurzburg. In Hungary, Jews were attacked in Trier, Metz, Prague, Ratisbon, and Nitra before the king of Hungary stopped the Jew-killers. Would-be Crusaders in England picked up the idea and massacred Jews in London, York, Stamford, and Norwich; only Winchester Jews were safe.
The killing didn't stop in Europe. When the Crusaders made it to the Holy Lands, they killed Jews even more enthusiastically than they killed Muslims; the Jews in Jerusalem were basically wiped out, in generally upleasant ways. This pattern lasted throughout the Crusades, as far as I can tell, but seldom shows up in the text books.