This is a modified version of gangleri's map, using Winner's base map. I've added another category for countries where there's violent ethnic conflict/ tension, but not a full-blown secessionist conflict.
Great job! Here some changes and their justification:
Angola: If the cabindan rebels are not a strong and highly militarized secessionist movement, then you tell me who is.
Comoros: Anjouan was invaded in 2008, so I think that Comoros no longer belong to the dark red category.
Democratic Republic of the Congo: Sporadic episodes of violence in Katanga, North Kivu and South Kivu.
Finland: Åland falls in the category of minor secessionism, IMHO.
Iraq, Iran and Syria: There's activity of the PKK in these three countries too, so I think they also belong to the same category as Turkey. Moreover, Iran has also the Baluchistan thing.
Mali: There were some episodes of violence during the Tuareg rebellion and since the situation is still pretty hot in Niger, I think that Tuaregs in Mali still belong to the red category, unlike those in Algeria, Libya and Burkina Faso.
Romania: Szekely is more an autonomist movement than a secessionist one.
St. Kitts and Nevis: There's minor secessionist movement in Nevis.
Serbia: Kosovo may be compared to Transnistiria, Abkhazia, South Ossetia and Nagorno-Karabakh, so it belong to their same category.
Yemen: Southern yemeni secessionist violence is sporadic only and the tribal conflicts in Aden and Dhofar are of autonomist nature.
Besides, are you sure that Uzbekistan should be blue? I'm not sure if the Karakalpakstan secessionist movement is relevant or not.