This is a really, really complex question.

First of all, saying asking about the collective position of "the Jews" is almost as broad as asking about the collective position of "the Christians" or "the Europeans." The Jewish population may have had a common religion, but the Jews of Spain and the Jews of Poland had about as much in common as, well, Spaniards and Poles.

In general, though, if you were to put together an 12-Century Jewish focus group, present all sides and ask for their preference, I'm pretty confident they would have favored the Muslims over the Christians. As a rule, until pretty recently, the Jews living under Muslim rule were treated much better than the Jews living under Christian rule. In Muslim lands, Jews were generally second-class citizens, but they were citizens. They had legal rights and protection. In medieval Christian territories, in contrast, they had none. Medieval Jewish history in Europe is one of pogroms, ransoms, and expulsions. In Muslim lands in the same time period, you have things like the Golden Age of Muslim Spain, where Jews were a valued part of society, or guys like Maimonides, the highly respected personal physician to the Sultan of Cairo. Of course there are exceptions, but the general trend was that life was much better for Jews when Muslims were in charge.

In terms of how the Crusades affected the Jews specifically: the Jews of the Holy Land often fought alongside their Muslim neighbors to defend their homes. The force that defended Haifa from a month-long siege during the First Crusade was almost entirely Jewish, and the Jews of Jerusalem defended the walls during that Crusade as well. They were massacred.

Jews of Europe also suffered a great deal. There were lots of pogroms, lots of violence against Jews. When you've got the Church preaching for a Crusade against Infidels, why on earth would you go marching across half the world to fight against non-Christians while ignoring the ones that live close by?

It was around this time that the Blood Libel first appeared, as well. It has different variations, but in general it's the belief that Jews kill Christians (usually children) and use their blood, usually to make matzoh. (As an aside, since it's Passover, anyone who has ever had a bite of matzoh will see how ridiculous that is. Matzoh is the least interesting food ever conceived. Blood would greatly improve it) Anyway, the Blood Libel first appeared in 12th Century England. I don't have anything tying it directly to the Crusades, I'm mentioning it more as an indicator of the flavor of the times.

A few sources: Towards a Definition of Antisemitism by Gavin Langmuir; In the Year 1096: The First Crusade and the Jews by Robert Chazan.