Somalia

Ongoing conflict since 1991. Seculars vs Muslims (and Christian Ethiopians), with US interventions and inter-tribal allegiances affecting the situation.
 
After the long and cruel dictatorship of Said Barre 1960-1991, factional fighting broke out and conditions in the country deteriorated. 300,000 dead, 1.5m displaced, and famine. There were UN and US humanitarian interventions 1992-95, which failed. This was followed by warlordism and disarray, also harbouring jihadis responsible for terror attacks in Kenya (where many Somali refugees had fled).
 
In 2004 a transitional government was formed, gaining little headway. Islamist militias took control in 2006, restoring some order, but they eclipsed the government and attracted opposition from those who disliked their moral strictness. USA linked the Islamists to al Qa'eda, backing an Ethiopian (Christian) intervention which removed the Islamists.
 
A war started which is not concluded, in which the Islamists are increasingly prevailing. In late 2008 Ethiopia declared a wish to withdraw, which leaves Somalia open to a Muslim takeover. Clan rivalries remain. Somalia has also become a haven for high-tech pirates, raiding ships in the key shipping lanes off Somalia, leading to the Suez Canal - some acts of piracy have been dramatic.
 
International peacekeepers are reluctant to enter this complex situation. There is an ongoing risk of famine and war escalation, and there are over 1m refugees - "the world’s most pressing humanitarian emergency". Currently the country is divided between two main jihadi groups, the 'transitional government' and various tribal territories, and the Ethiopian- and Western-backed transitional government is waning, with control only in Mogadishu and Baidoa. This is not primarily a religious war, but jihadi forces plus Christian influences (Ethiopia and USA) are involved, and side-effects are leaking out in neighbouring areas and sea-lanes, making this local conflict global in context.
 

Links:

New Internationalist Country Profiles
Reuters Alertnet: Somalia
Wikipedia: War in Somalia