This is probably a poor subject for a first post in GD, but I'm opinionated and can't keep my mouth shut, so... ;D
A few things that I'd like to say before I go in to this: Ultimately, I am not anti-religion. Religious organizations have, in the past, been extremely strong mechanisms for social change. Because of a focus on in-group unity, religious organizations can mobilize large groups of people in ways that other organizations cannot. However, I would argue that this has to do little with the religion itself, but with the feeling of belonging that religions can promote.
To the actual discussion:
Sarcastro, I feel, has hit the nail on the head win regards to Northern Ireland. I won't address that.
I would say that most religious conflicts have underlying social reasons, but the conflicts would be nowhere near as extreme without religion. Not only does religion contribute to in-group/out-group hostility, as Sarcastro pointed out, but religion provides justification. Religion, particularly Abrahamic religions, label those outside of the religion as infidels and heretics, and by fighting them, one is doing "the right thing."
An example that is particularly prevalent today is that of radical and fundamentalist Islam. The suicide bombers and jihadists genuinely
believe
that their actions will bring them to heaven. Before the 9/11 attacks, the hijackers bathed themselves in perfumes and shaved their bodies in preparation for the afterlife. Without the promise of paradise in the afterlife, would they have been as willing to take those lives? Without the justification that the Western world is populated by infidel, who are less than human, would they be so easy to kill?
I would argue that, if actual religion were taken out of the equation but the in-group/out-group hostility remained, the conflicts in the middle east would be drastically less severe.
At the same time, social problems DID let (to use Ayaan Hirsi Ali's words) the "jihadist genie" out of the bottle. Radicalism can lay latent for centuries and decades- there, but sleeping; radical, but not fighting. I'm fond of analogies, so let's go with this: Social issues are the trigger on the gun of religious fundamentalism, however, it is the religion itself that allows the bullet to gain speed.