The bloody christian crusades killed thousands and thousands of innocent Jews...
http://www.torah.org/features/holydays/omer2.htmlPROPHETIC SUFFERINGS
In the times of the Crusades, there were more tragedies of immense proportions during the sefirah. In 1095 CE, during the sefirah, the Jews of over one hundred Ashkenazic communities were mercilessly massacred by the first Crusade. These included the large communities of the cities of Shair, Worms, and Magenca. In Shabbat prayer services between Passover and Shavuot, special lamentations are added to the liturgy to commemorate these massacres. Also, the prayer "Av HaRachamim," which is said all year round on Shabbat to eulogize Jewish martyrs, was composed primarily as a result of the devastation caused by the first Crusade. In some communities, "Av HaRachamim" is said only during the sefirah.
Fifty years later the second Crusade set out, between Passover and Shavuot. Again, thousands of Jews were massacred. According to Polish Jewish tradition, a special hymn written about this tragedy is to be said in the very beginning of the sefirah -- on the first Shabbat after Passover.
So, too, many of the "transports" to the death camps during the Holocaust were carried out during the sefirah.
Also, every year, the public reading of Parashat Bechukosai falls during the sefirah. It is said in the name of the Vilna Gaon that this was intentional, for this Torah portion prophetically describes the terrible suffering that the Jewish people would have to endure for failing to remain faithful to the Torah. The Sages who lived long before the Crusades, and before the times of Rabbi Akiva, too, instituted the weekly readings. According to the Vilna Gaon, the Sages of old foresaw that the period between Passover and Shavuot would be filled with sadness. Therefore they intentionally scheduled Bechukosai to be read during this period in particular, to clarify to the nation what, in fact, would be the cause for its woes.