The European wars of religion (Schmalkadic War, German Peasants' War, Second War of Kappel, Eighty Years' War, French Wars of Religion, Thirty Years War, Wars of the Three Kingdoms).
These were wars over the effort of leaders and to either expand (Henry VIII, German Princes, Cavinist Geneva) or protect (The Holy Roman Emperor, the Pope, the French kings) temporal power.
Sudanese Civil Wars were between Muslims in the north and Christians in the south, which was one reason for the split.
Most Southern Sudanese adhere to traditional religions. This was about the North attempting to suppress the South in order to maintain control over its natural resources, as well as a good deal of ethnicist Arabism.
The Crusades, of course; all of them, not just the ones to Jerusalem, like the Cathar and Northern Crusades.
Efforts of leaders, again, to expand their powers.
The Lebanese Civil War pitted Sunnis against Shiites against Christians.
The Christians wanted to maintain the confessionalist status quo that had given them disproportionate power based off dated censuses, while the the others both wanted to increase their powers.
The Reconquista certainly had religious elements involved.
Elements or motives? It was a war over who would control Iberia.
Muhammed's wars are certainly arguable as such, and subsequent conquests as well up to the Great Turkish War.
What Nathan said, and imperial motives thereafter.
The operations of the Irgun were religiously motivated in Palestine in 1948, and the subsequent Palestine-Israel conflict can be seen as a religious war.
Come on, this is an ethnic fight over land- over whom it belongs. Jews are not only a religious group, but an ethnic one.
The separation of India and Pakistan was mostly for religious reasons, and Sikh separatists in India fought for their religion as well.
These have more to do with, again, cultural identities than actual religion.
The Abyssinian-Adal War in 1529-1559 was a religious war between the Muslim Somalis and non-Muslim Ethiopians.
Not even ethnic, but national. You are gravely mistaken if you assume Ethiopia, even the northern highlands, to be either ethnically or religiously homogeneous
The series of riots in Nigeria over the past few decades has typically had religious undertones.
These are again ethnic conflicts- pitting the northern peoples against the southerners. Nigeria has been a story of ethnic conflict- that of Northerners seeking to exert dominance over the resource-rich south and to a limited extent vice versa.
The Buddhist Uprising was a purely religious uprising in Vietnam.
This is the most likely, but still it stemmed from Diem's concerns of Buddhists' loyalty (or lack thereof) as opposed to his having a problem with them purely because he was Catholic and they were not.
In not one of these wars was one side fighting over religious doctrine or because X group was heathen or the like. Similarly, the Lebanese Civil War would not have been any different had you replaced religious groups with ethnic groups- they are in most places to a degree synonymous. Conversely, had the only thing