I'm reading The First Crusades by Steven Runciman, preparing for the Medieval History we'll study this year. I had thought that all of the fighting took place in the Middle East, but it turns out that the first crusaders to get going, the People's Crusade, decided that there was no point in waiting and started killing Jews in Germany; although the Jews were generally under the protection of the local bishop, the bishops were unable or unwilling to protect them. The killing only stopped when the crusaders got to Hungary, where the army refused to allow it.
The usual exhortation in the massacres was that the Jews had killed Christ and deserved to be killed in return. But since Christ was also Jewish, it seems more likely that the real reasons were economic rather than religious. The Jews were the only group allowed to charge interest (usury was prohibited to Christians), so nearly all loans were made by them; this meant that churches, nobles, kings, and peasants were all indebted to them - and no one likes the person they owe money to. The charge of Christ-killing appealed to the emotions of the crusaders, but the massacres were possible because the medieval Jews were already marginalized and distrusted.