Separatism is usually based on either language or religion. In Yugoslavia Slovenia, Kosovo and Macedonia wanted to separate on linguistic criteria, while Croatia and Bosnia used religious arguments. I think it is good to make a distinction between both as such separations work out very differently.
As countries modernize there is a natural tendency towards linguistic separation. As countries modernise they become increasingly dependent on documents and communication. As a consequence it become increasingly expensive to provide services in all languages. This applies also to the individual people who need to speak more than one language in order to qualify for their jobs. Adding to this is that with the advance of international languages like English fewer people learn the languages of neighbouring ethnic groups. You see the same in Western countries. For example Belgium has an official language border. The only area that is still officially bilangual - Brussel - has become de facto French speaking (about 90%). And much of the communication between the french and dutch speaking communities is nowadays in english. In Canada too Quebec has adopted a policy that stresses the french speaking character of the province.
Most people understand this logic of linguistic separation. The separation of Slovenia and Macedonia went nearly effortless. Kosovo is a bit more complicated as the population is more mixed. But the main problem there is that the international community is pushing for terms of separation that are seen as extremely unfair by the Serb side.
Religious separation is a completely different thing. Unlike linguistic differences there are no special policies necessary to keep a multi-religious society working. One only needs to keep track that there isn't too much discrimination. With religious differences people tend to live much more mixed and are often not even aware of their differences. However, once the process of separation starts it tends to be self-reinforcing.
Separatism is primarily motivated by economic motives. Usually it are the rich provinces that believe they would be better of when they no longer had to subsidize the poorer provinces. But - as Yugoslavia demonstrated - the promise of financial support by other countries and membership of a rich club like the EU will do the trick too. However, an economic motive is not enough - it looks egoistic and it would give all the people who will be disadvantaged a claim for compensation. And so there is a need for some ideological justification.
This is usually found in ethnic differences. With linguistic differences this is easy to do and generally accepted. But invoking religious differences is rather unconvincing. It is probably no coincidence that both Bosnia and Croatia invented new languages to strengthen their claim of specialness. Another trick is provoking conflicts with for example "loyalty declarations" and distoring history in a way that is bound to anger the others.
Separation has two opposite effects. One the one hands it ends a conflict, but on the other hand it stresses the differences between people and often leads to the complete disappearance of the minority group from the separated territory.
With linguistic separation the balance is usually on the positive side. There is little need for stressing the differences as they are clear and the population often already lives separated. And so the polarisation stays restricted. But with religious separatism the damage done is usually much more severe and one needs to wonder whether it is worth the trouble.
I think that for the international community the main lesson should be to pay more attention to the details of discrimination. In the case if Yugoslavia this should have started with Slovenia. The case of the "erased" might have been considered too tiny when Slovenia was the only separating province. But in the case of Yugoslavia it set a bad precedent and should have been punished with heavy sanctions and refusal of recognition. Similarly, Croatia's "loyalty declarations" and mass firings of Serbs should have been heavily critized and sanctioned.
I have always considered it stupid to see the dissolution of Yugoslavia as desirable because the Serbs had become too dominating. Bosnia and Croatia faced exactly the same dilemma's of dominant groups and minority rights. Interestingly both before and after the dissolution there was little international attention for discrimination in Yugoslavia.
Instead all the attention went to Serb nationalism. I found this rather strange as I see nationalism as a sign of democratisation. Besides their crazy points the Serb nationalists had some good points that really needed to be repaired. It is often stated that the Croat and Slovene nationalism was a reaction against the Serb nationalism. But I think that is only true for a minor part. Mostly it was just a matter of long repressed nationalists who finally found a good excuse to seek the spotlight again. Nothing wrong - they had their good points too - but I have never understood the eagerness with some some diplomats adopted their case. It would have been better to use them as the basis for negotiations and not accept any outcome that did not protect all groups involved.
The advantage of a stable situation is that it usually brings a reasonable standard of human rights. Revolutions however bring radicals to power and a general deteriorisation of human rights. The first time it went wrong in Yugoslavia was the Serb take-over in Kosovo. But instead of concluding from this that revolutions were not desirable the West promoted its own revolutions in Slovenia, Croatia, etc. And even today we see internationals obsessed with constitutional reforms in Bosnia - while they ignore the dynamics of equality and discrimination in the inter-ethnic relations.
In Iraq the Americans made a false start with the dismissal of the whole army and the de-Baathisation - two measures clearly meant to trouble the Sunnites. Nowadays they are a bit wiser but they face the challenge to convince a government dominated by Shiite radicals that they should treat the Sunnites as equals. I think they have only a chance when they make it core of their mission. They should really believe that the best thing that they can leave behind is a democratic Iraq where everyone is treated equally. At the moment the policy of appeasement of the Sunnites is mostly a tactical ploy. The nationalist clique around Cheney would still prefer to keep their radical Shiites happy and has only (temporarily?) changed because the price seemed too high.