Doesn't look good, according to Anna Matveeva:

The long-term prospects are worrying, as the Uzbek minority realises that it is largely on its own with its problems. A renewal of the summer's clashes is at present is unlikely, as the community is shocked and scared. There are three possible templates for the future: that of Sri Lanka, where a powerful guerrilla organisation emerged after ethnic riots; that of Chechnya, where a nascent nationalist movement fell prey to Islamist networks; and that of Uzbekistan, which reacted to Andijan with overwhelming repression. None of these is very inspiring.

To resolve the situation, the ruling elite have to show a determined commitment to the ideology of multi-ethnic society instead of a "return to democracy" based on the titular group supremacy. Policy on interethnic relations and minority issues needs to be articulated, and a mechanism of reconciliation should be established to support it.

Update: Mobs of armed men torched Uzbek neighborhoods on Friday, leaving at least 49 people dead and 650 wounded. Thousands of ethnic Uzbeks have fled west towards the border. Riots are now taking place in Osh and the country's capital, Bishkek. 
 
The interim government in Kyrgyzstan declared a state of emergency after twenty-three people were killed yesterday in riots in the city of Osh. Several sources have speculated that the violence in this volatile southern region may have involved clashes with ethnic Uzbeks. Even if there was not an ethnic overtone to the conflict, it is still an ominous sign for the stability of the fragile administration in Bishkek and the Central Asian region as a whole. 

Much of the southern portion of Kyrgyzstan is divided between large Uzbek and Kyrgyz communities. Historically, these groups have battled each other over agriculturally viable land and political power. In June 1990, this turmoil sparked a riot in Osh in which over 300 people died and thousands were injured before the Red Army stepped into stop the bloodshed.

Since protestors deposed President Bakiyev in April, the central government’s control in the region has remained tenuous at best. The Uzbek community has so far refused to take sides in the dispute, but it fears that the growing authority vacuum could trigger violent antagonism. Unless the Otunbayeva administration can restore calm in this chaotic region, political unrest could become ethnically charged. It is up to the central government to decisively quell the violence before it takes on a life of its own. No one wants to see ethnic separatism tear the 'stans apart.

Just days after protests began in the northwestern Kyrgyz city of Talas it appears that the opposition has won a stunning victory. If the Twitter pundits (Twitdits?) are to be believed, the popular coup in Bishkek has much broader significance. According to the computer savvy masses, Tulip Revolution II should serve as a model for every other nascent democratization movement from Iran ("that's how you do it #iranianelection" seems to be a common sentiment) to Azerbaijan.

Before everyone gets carried away, let’s take a step back and review. The events in Kyrgyzstan are many things, but a model is not one of them. Here are four reasons why:

1. The Kyrgyz have a strong history of staging effective protests. In 1993, protests brought down former Prime Minister Tursunbek Chyngyshev.  In 2002, protesters forced then President Akayev to begin the process of reforming the country’s constitution. And of course there is the 2005 Tulip Revolution, which current opposition leader Roza Otunbaeva played a key role in organizing. It’s much easier to get a crowd together when people believe they are likely to succeed.

2. Kyrgyzstan lacks the natural resource wealth that allows governments in many other authoritarian or semi-authoritarian states to effectively quell internal dissent. And while I hesitate to use the word “easier” when talking about coups and revolutions in the former Soviet Union, it is clear that the Bakiyev regime was vulnerable because of it.

3. The protesters were backed by a segment of the Kyrgyzstan’s political elite and if reports out of Bishkek are true they were able to quickly co-opt members of the security services. 

4. The Bakiyev government wasn't particularly bright. Deciding to increase utility prices by 200% while publicly flaunting your corruption-based wealth  is a sure way to stir up popular unrest.

-Evan

AP has a detailed report here. Highlights:

The opposition and its supporters appeared to gain the upper hand after nightfall, and an Associated Press reporter saw opposition leader Keneshbek Duishebayev sitting in the office of the chief of the National Security Agency, Kyrgyzstan's successor to the Soviet KGB. Duishebayev issued orders on the phone to people Duishebayev said were security agents. He also gave orders to a uniformed special forces commando.

[...]

The anti-government forces in Kyrgyzstan were in disarray until recent widespread anger over the 200 percent hike in electricity and heating gas bills helped unify them and galvanize support. Many of Wednesday's protesters were men from poor villages, including some who had come to the capital to live and work on construction sites. Already struggling, they were outraged by the utility bill hikes and were easily stirred up by opposition claims of corruption in Bakiyev's circle.

Update: The Boston Globe has a stunning photoset here.
Update 2: RFE/RL's Bruce Pannier breaks it down on Al Jazeera.