One lasting negative effect of the Crusades was the political and religious relationship between Christians and Muslims. The general purpose of the Crusades was to "win back the Holy Land" from Islam. So right from the start you have a war whose primary goal or motivation is nominally a religious one instead of a political or territorial dispute. The case can be made that at the time, religion (Catholicism) and political government were more or less one and the same. That's true; however, your question asked about lasting effects. Like any war, it was brutal, violent, and full of war atrocities. This time though it was being done "in the name of God." So what was present for many years after the Crusades (and even today) is a strained relationship between Judeo-Christians and Muslims that often leads to violence.