One of the primary reasons for these conflicts was over religious differences between members of the Christian faith against Muslims and others. Originally the crusades were intended to recapture Jerusalem and other territories - which over the centuries had come into Muslim hands. The first crusade was held in the late 11th century, from 1094 to 1099. For the next two centuries there was an entire series of crusades.
Saladin was a Muslim general whose forces recaptured Jerusalem from the crusaders in the 12th century. Approximately 1000 years after his death, Starfleet named the Saladin-class starships after him. (TOS reference: Star Fleet Technical Manual)
When the Hirogen captured USS Voyager, they used the ship's holodecks to study the races of the United Federation of Planets, whom they considered prey. One of the early simulations was one that took place during the crusades on Earth. The Doctor remarked to Seven of Nine that she should've seen herself after being injured in the crusades simulation. (VOY episode: "The Killing Game, Part I")