One, South Sudan (possibly to be named "New Sudan") is likely to come into being around 2011. It is essentially full autonomous already and is acting like its own country, developing its own diplomatic ties via Kenya, and strong economic ties with Uganda. Final details largely concern its control over White Nile water and division of oil wealth. The largely Christian and animist region with relatively fertile farming has been autonomous since about 2005, after a long and deadly civil war that killed about 2 million people. It has sought autonomy from the military influenced, largely Islamic leadership of Sudan.
The Darfur region in the West of Sudan, which has provoked international outrage over genocidal efforts by local Arab militias and collusion with the national government is not part of South Sudan and poses separate issues. The Arab Muslim v. Christian/animist dynamic is essentially the same. But, ethically, Darfur is more mixed (or was before genocidal campaigns killed 200,000 people and sent another 2,000,000 into refugee camps), and economic survival in relatively barren Darfur is a dicey proposition in the best of times.
The other is Kosovo. There, about 90% of people in this autonomous region of Serbia are ethically Albanian Muslims, and only U.S. led NATO intervention and U.N. peacekeepers have prevented Serbian massacres (Serbia, of course, sponsored genocide largely directed as Bosnian Muslims in the Bosnian civil war, and is largely Orthodox Christian religiously).
Serbia has based its claim to Kosovo largely on a desire to protect sites important to Serbia historically and to protect a Serbian minority in Kosovo, but as much as anything else, it is a matter of national pride to hold onto Kosovo, as Serbia has been willing to cede almost everything be sovereignty in interminable negotiations over the province's status. The international community has held off on granting Kosovo independence over Serbia's objection essentially entirely due to Russia's objections. But, the international community is manuevering diplomatically to circumvent Russia's objections and give Kosovo the independence that its residents overwhelmingly desire.
Montenegro recently left its nominal federation with Serbia.
The situation in Bosnia, by the way, while stabilized for now, is still unfinished business. The U.N. still keeps the peace, and in practice, Bosnia is essentially two countries -- a Serbian region (mostly to the East and North), and a Muslim-Croat federation (mostly to the West and South). This division has religious dimensions as well. Croatia is largely Roman Catholic.
From an outsider's view, the obvious thing to do seems to be to grant Kosovo independence, while permitting the Bosnia Serb autonomous region to merge with contiguous Serbia proper (possibly merging a couple of islands of isolated Bosnian Croat federation territory on the Croatian border with Croatia). But, apparently, it isn't that easy, as the international community doesn't want to open the cauldron of changing national borders without mutual consent or appearing to reward genocidal tactics.
One reason that the situations in Sudan and Kosovo matter in the larger world is that they create precedents for the international community that are relevant in the Middle East.
The Kurdish region of Iraq is in a similar de facto autonomous, but legally non-sovereign state to Kosovo and South Sudan, and like these two other regions would very much like to be its own state. Also, like South Sudan, water and oil right negotiations are relevant to its autonomy.
Independence for these regions would strengthen both the Kurdish case and the argument that the rest of Iraq ought to be partitioned as well.
These aren't, of course, the only restive autonomous regions in the world.
In the developed world, politics seem to have calmed a number of autonomous areas by granting them sufficient autonomy. Quebec, Puerto Rico, Basque Spain, Castille, Galacia, Scotland, Wales, and Northern Ireland all seem willing to accept their lot for now. Taiwan's love-hate relationship with China seems to be swinging towards the love side, and Hong Kong seems to be managing despite the restoration of Chinese sovereignty over it. Cyprus, however, still seems to be taking baby steps towards harmony.
This isn't to say that all is well in the world. Columbia's central government and the region controlled by the FARC seem to be in a standoff. The last that I heard, Muslim majority areas in the Southern Philippines were as committed to a violent struggle for independence as ever. Strife between Muslims and non-Muslims also appears to be at the root of autonomy motivated strife in Thailand and Nigeria. Other West African nations have also experienced civil war and regional tensions rooted in splits between those in the Muslim North and those in Christian/animist Southern regions, but with civil wars reduced to a simmer or ended in Senegal, Sierra Leone, Liberia and Ivory Coast, and averted in Mali, these fracture lines may not emerge again for some time. Of course, Israeli-Palestinian tensions continue unabated as they have for many decades now.
Kashmir in Northern India is not at peace, nor are the "tribal" regions of Pakistan content with their status vis the central government although political approaches have softened their usual disregard for central authority. And, the Kurds of Turkey still want out of the nation to form their own Kurdish country.
Somolia is largely a country without a government but seems to be well along in the process of reconsolidation with Ethiopian backing of a weak national government. Regional and religious separationist movements in Algeria and Morocco-Western Sahara seem to have quieted down lately. Unrest in independence minded Aceh, Indonesia is apparently easing, but I've heard no indications that Sri Lanka is near the end of its long standing bloody civil war.
Maoist insurgencies in Northeast India also appear to be alive and well, and while not an issue of national boundaries, the Maoist insurgency in Nepal also appears to be in full swing. Tibet appears irrevocably conquered by China with insurgency and independence efforts their crushed and migration from the East underway in part in an effort to wipe out the region's distinct identity.
Then, there are other messes left behind in the wake of the Soviet Union's dissolution. Russia appears to have strong designs on Belarus. Ukraine is deeply divided, largely on an East-West axis. Moldova also appears to be divided on similar lines, despite the fact that it is itself tiny. Chechnya still longs to be free of its Russian yoke. And, the other splinters of division in the Caucusus are too complicated to follow without a program. As Wikipedia explains:
The nation-states that compose the Caucasus today are the post-Soviet states Georgia, Armenia, and Azerbaijan; and various parts of Russia. The Russian divisions include Krasnodar Krai, Stavropol Krai, and the autonomous republics of Adygea, Kalmykia, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia, Ingushetia, Chechnya, and Dagestan. Three territories in the region claim independence but are not generally acknowledged as nation-states by the international community: Abkhazia, Nagorno-Karabakh and South Ossetia.
I'm sure I've missed a few restive autonomous regions here and there. This isn't to say that there aren't consolidating influences afoot as well. The European Union is increasingly becoming a nation, rather than a mere alliance between fully autonmous nation-states. The Caribbean, Latin America and parts of Africa are trying to emulate the European Union's success on that score. But, on the whole, it seems like there are more pressures for division than national union afoot in the world.