With hindsight one can now see that there has been a growing pattern of Sunni-Shia conflict emerging in the Middle East, which to some degree paralells the Moslem-Jewish conflict and may be far more bitter. Iraq seems to have been the spark that ignited the conflict, and it may well be that it won't extend beyond Syria-Lebanon.
Round I: The Iraq - Iran war (1980 - 1988)
In 1980 the Sunni-dominated Iraqi regime of Saddam Hussein invaded Shia-dominated Iran, then fresh from a religious revolution. This lead to the Iraq-Iraq war and the deaths of hundreds of thousands of soldiers and civillians in both Iraq and Iran. The invasion was the product of a long history of tension and border disputes between the two countries, much revolving round Kurdish revolts in Iraq, however the revolution in Iran had radicalized the Shia third of Iraq and led to growing attacks on the regime by Iraqi Shia radicals.
The Iraq-Iraq war was not purely a Sunni-Shia conflict, and the Iraqi regime was not overtly religious, but the creation of a regime in Iran whose ideology was formally religious-national meant that any conflict involving that regime risked escalating into ethno-religous conflict.
Round II: The Iraqi civil war / insurgency (2006 - 2008)
The Ottoman empire was a religious empire based on Sunni Islam and during the centuries of Ottoman rule in Iraq, the Iraqi Shia were a neglected religious group. The British tapped into existing elites and established a state in which the Sunnis continued to dominate, although Shia were the majority.
The 2003 US invasion and the forcible implementation of democracy in Iraq led to sudden Shia domination, since the Shia are the majority of the Iraqi population. Religious-nationalism formed a focal point of opposition to the US presence and neatly gelled with the extreme anti-civilian violence of Al-Qaeda whose religious xenophobia turned out to be directed against Shia Moslems no less then non Moslems. As a result Shia and Sunni militias fought each other as they fought the USA, but while they only targeted the US occupying army, they mercilessly attacked each other's civilian population. For both sides the USA was the prime target, but Shia-Sunni warfare was now openly sectarian and extremely bitter.
Round III: War in Syria: All out Sunni=Shia warfare. (2011 - Present)
When Hizbullah, Iran's Lebanese Shia militia, started fighting on behalf of the Syrian regime, the conflict there turned into an almost purely sectarian war. One can now see that each round of conflict since the Iran Iraq war has incorporated greater Sunni-Shia conflict and that this is now becoming the Middle-East's dominant conflict.