The Crusades is the classic example, though many would counter that the Muslims instigated those wars and that the Crusades was merely a call to join forces - not a call for a new war, but a call to coordinate the ongoing defensive wars against the continual onslaught of Muslim forces.
The wars between Protestants and Catholics during the 16th and 17th centuries are also often cited. However, more often those are cases of wars started by or for the sake of political gain rather than religious conviction or under religious direction.
Probably the best answer is the various inquisitions undertaken by the Roman Catholic Church. Even many of those, however, would be VERY questionable, the political goals of local leaders often being foremost.
The bottom line is that religion is rarely responsible for war; rather, normally religion is used by political leaders to support wars that are actually begun for gain:
- a combination of the above