There are, of course, actual figures available on this. I commend the totally comprehensive datasets generated by Uppsala University, especially as processed by the Human Security Project, for anyone who wants to get into this subject in depth; the figures below are for the latest year they cover in detail, 2005, where they find 17,458 deaths worldwide as a result of all types of political violence, including war, in 34 different countries. I won't review them all here, but the top thirteen, accounting for 84% of the death toll, were as follows:
Iraq. 3,388. While religion is an element in this, I think that there is just a little more going on as well. ETA: this estimate is way below that provided by other sources. The Iraq Body Count has 14,000 civilian deaths in 2005, not to mention the coalition forces.
India. 1,823. Of these, 80% (1464) relate to the conflict in Kashmir, which certainly started and continues as a conflict about religious identity, though again with other elements involved.
Nepal. 1,474. Only counts as religious if Maoism counts as a religion.
Colombia. 1,438. All parties are from the same religious background (Catholics).
Afghanistan. 1,329. Again, there are religious elements, but as with Iraq there is a bit more going on.
Sudan. 1,015. Almost entirely related to Darfur, where all sides are nominally Sunni Muslims.
Uganda. 997. Yep, this is definitely a religious conflict, in that the repulsive Joseph Kony claims to be receiving instructions directly from God.
Ethiopia. 918. Arguable, in that 641 of these relate to the conflict between the (Christian) government and (Muslim) Somalis in the Ogaden province; but there is more than just religion to this particular situation.
Russia. 668. As with Ethiopia, just because Russians have a Christian background and Chechens an Islamic background doesn't make this a religious conflict.
Thailand. 490. Once again, the Patani insurgents are Muslims and the government Buddhist, but there is more to this one than religion.
Philippines. 418. This is half and half: 237 due to the conflict with Communist insurgents (see Nepal), and 181 due to the Muslim insurgency in Mindanao, where, again, religious identity is a factor but not the only one.
Somalia. 370. No religious difference between the factions; all are Sunni Muslims.
Turkey. 359. Minimal religious difference between the Turkish government forces and the Kurds, both being somewhat non-fundamentalist Muslims.
If you're wondering what happened to Israel/Palestine, 2005 was a relatively quiet year there with "only" 176 deaths due to political violence. The full list of other conflicts tallied by country for 2005 is as follows: Burundi (353); Myanmar/Burma (260); Algeria (253); Nigeria (217); Indonesia (213); Mexico (180); Israel/Palestine (176); Côte d'Ivoire (141); Egypt (124); Sri Lanka (115); Pakistan (111); Chad (100); Democratic Republic of the Congo (92); Rwanda (also 92); Kenya (68); Jordan (62); Guatemala (54); Haiti (40); Brazil (35); Saudi Arabia (31); Iran (28); Azerbaijan (26).
Basically, in all of these cases apart from Uganda (and just possibly Kashmir), to say that the conflict is caused by religion is misleading and wrong. In almost all cases, the drivers of conflict are competition for resources, fuelled by distrust of the idea of government by or with the other side on the basis of past historical experience. In some of the worst cases of violence (Iraqi locally recruited government forces vs local insurgents, Colombia, Darfur) people are fighting their co-religionists. To blithely say that religion is the worst cause of conflict worldwide is incorrect and patronising, suggesting that the solution is for the warring parties to become enlightened like Richard Dawkins, and that if they won't there is little to be done about it. It is the excuse that was used for non-intervention in the Bosnian war. It is bad analysis of the problem which leads to (or at least excuses) very bad policy decisions.
As for Joseph Kony, he is surely one of the best advertisements for the international war crimes tribunal imaginable.