NATO bombed Serb positions in BiH in 1995 essentially breaking the Serb strangle hold over BiH. As for Croatia, Serbia just lacked the power projection to strike deep into Croat territory, especially while simultaneously dealing with uprisings in BiH, Kosovo, a secessionist gov't in Macedonia and a deteriation of realations with the people of Vojvodina in Serbias north. Croatia declared independence and two weeks later Germany recoognized it, followed by the EEC a month later. Germany supplied Croatia any weapons they wanted from the E. German stockpiles. Its also important to note Yugoslavia had a policy of conscription and a huge army prior to the outbreak of hostilities, most of the male population was familiar with weapons and tactics. As a side note the Yugoslav army tended to station its troops in regions they were from so once all these countries started declaring independence they came with loyal ready made armies.

The Death of Yugoslavia, BBC, 1995.

Jane's International Defense Directory, 1998.

I think your confusing the Yugoslav wars (1992-1995) with the Kosovo war (1998-1999).

In a related know what role did private military companies play in the 1991/1996 era of the war

Yugoslav National Army (JNA) and its heavy equipment was largely owned by Serbia, especially early in the war.

The JNA had largely withdrawn from Croatia and Bosnia Herzegovina by the middle of 1992. 1

The majority of the population of the countries at war was Serbian, and Croatia and Bosnia both had significant Serbian minorities and self-declared Serbian states within them (Republika Srpska Krajina and Republika Srpska Krajina).

If you are including Serbia, yes, but as I stated above, the JNA had primarily withdrawn by the middle of 1992, so we can count Serbia out as a country.

The Bosniaks had arms smuggled to them from foreign countries, but again this takes time. NATO support did not come until 1999, 8 years after the wars begun.

It also takes time for the Serbs to put together their paramilitary forces. The Croatian War actually simmered down between the end of 1992 and 1995, allowing Franjo Tudjman and his government to smuggle in weapons in preparation for the big Croatian offensive in 1995. 2

NATO did intervene in Bosnia late in the war in order to bring the Serbs to the negotiating table. This probably influenced the decision to bomb Serbia a few years later during the Kosovo War. But that's a whole other subject.

So, to recap:

JNA withdrew from the conflicts, leaving only Serb militias.

Ceasefires and significant amount of weapon smuggling aided the independence factions.

Short answer is - war crimes. At the start of the war Serbs commited some of the most horrendous crimes in modern history, from rape camps, to murder of patients at Vukovar hospital and mass rape of Croat women. That changed the narrative of the war from simple civil war over separation from Yugoslavia to the war of survival. When the enemy takes no captives you have no option than to fight or die.

That created a huge discrepancy in unit morale between Serbs and their opponents.

Bosnia a short history - Noel Malcolm and Heavenly Serbia from myth to genocide

Whilst being comparably strong in material compared to its opponents the JNA and Serb paramilitaries had poor morale throughout the entire campaign, whereas Bosnians and Croats were fighting for their families' lives. An early example is the Ten Day War in Slovenia when JNA troops collapsed against a lightly-armed Slovenian territorial force.

The Serbs were poorly led and the strategy of months-long rolling artillery barrages had very little effect in actually advancing the line. The siege of Sarajevo is a good example of abysmal Serbian leadership as they did not take the city for the entire war. Debateably this is because the Serbian leadership did not want to overextend, especially in areas with Bosnian and Croatian (hostile) communities.

An interesting point to add is that due to a nuance from Titoist Yugoslavia, Bosnia contained a large portion of the country's military production. This meant the start of the war in Bosnia saw enormous gains by the Serbs as they rushed to secure as much of this production as possible, especially in Serb-majority areas.

You also touched upon the supply situation in Croatia and Bosnia and it should be worth noting that once the USA unilaterally ended the arms embargo Croatia made collosal gains in September-October 1995.

Noel Malcolm: Bosnia Mark Thompson: A Paper House, the End of Yugoslavia The Death of Yugoslavia (BBC) Heavenly Serbia: From Myth to Genocide

Just a quick late comment:

The Yugoslav Cold War defense strategy also played into the dynamics of the conflict. Yugoslavia, wedged between NATO and the Warsaw Pact (and Albania doing its own little crazy cult-state thing), feared an invasion either from the west or from the east. In either case it would be unable to stand up to the entire might of either alliance for a significant period of time. So the strategy was to train every man in basic military skills, even going so far as having high schoolers learn how to disassemble, clean, reassemble, and shoot small arms in required high school classes. Weapons caches were also hidden around the country. If either bloc invaded Yugoslavia, yeah they could take it, but against an entire country of guerillas they sure wouldn't be able to hold it. (This is compiled from a number of sources which I don't have on hand, but for one, this book notes it).

This strategy was also ideologically based. World War II in Yugoslavia was an occupation with a multiparty civil war going on underneath. The guerillas who ultimately came to power at the end of the World War and simultaneous civil war were the Partisans, communists; the Partisan leaders became the rulers of the new Yugoslavia. The story of their guerilla struggle during the War became part of the national mythology and also the source of legitimacy of the Yugoslav communist government. In short, guerilla fighting was the strategy because it was thought of as how Yugoslavs fight.

So essentially, OP's generally true statement "it takes time to apportion it out and train civilians how to use it" actually was not so accurate in the case of Yugoslavia.

On another note:

I politely disagree with the other commenter, /u/Hrulj , who pointed to war crimes as a major factor leading to poor Serb morale and ultimately contributing to their defeat. Though Serb forces almost certainly committed more atrocities than Bosniak or Croat forces during the Croatian and Bosnian Wars, those other forces committed atrocities too. Milosevic-controlled media streaming out of Belgrade convinced the whole of Serbia that Croatian Nazis and Bosniak Jihadists were coming to kill their children. Milosevic-controlled media also downplayed or denied Serb atrocities against other ethnic groups. So if the other commenter's argument is "Serb atrocities made Bosniaks and Croats feel like victims and filled them with righteous rage, which improved their morale and therefore fighting spirit," then I don't see why the reverse isn't also true-- real, imagined, manufactured, and exaggerated atrocities against Serbs made Serbs feel like victims and filled them with righteous rage as well. I would be interested in seeing what page or section of Malcolm's Bosnia: A Short History or Anzulovic's Heavenly Serbia: From Myth to Genocide that commenter is referring to for his/her argument.