In the beginning there was Stack Overflow, the programmer's Q&A site. It's been very successful, easily overtaking its competition. It's now the clear best choice for a place to ask questions and look for answers about programming.
After a few months, Stack Overflow spawned Server Fault (for system administration topics) and Super User (for computer user topics). They've been moderately successful, nothing like Stack Overflow, though: they've each accumulated 36,000 questions, while Stack Overflow has 640,000 so far.
Then they figured, why can't we handle any topics at all, and let anyone create their own site? And so Stack Exchange was born, a site where anyone could create a Q&A arena on whatever topic they wanted.
But it wasn't free, in fact, it seemed kind of expensive: $129/month. And the sites weren't taking off. It seemed that each step removed from programming questions meant a 20x drop-off in traffic. The Stack Overflow team (Joel Spolsky, Jeff Attwood and a bunch of others) are now looking for ways to extend their success, including getting some investment.
As part of their new plan, they've announced changes to Stack Exchange: Stack Exchange 2.0. Everything's free now, but the process for creating new sites has become as convoluted as a Politburo meeting. Interestingly, the comments on the announcement are mostly mad about the loss of the paid option, because a paid site is owned by its creator, while the free sites are not.
I think the new community creation process is way too heavyweight, especially where they require a certain number of users with a certain number karma points on existing sites to commit to a community before it will be created.
Overall, it's a familiar internet story: a startup creates something, people start using it, but then the business plan shifts, and users are left feeling abandoned. Small startups have to adapt to survive, but they don't want to piss off too many people along the way.
One interesting point in this whole thing: Joel has been very direct with people, telling them if they think they can do a better job building a community, they're welcome to use one of the Stack Overflow clones to do it. And there are a bunch of clones: Array Shift is built in Drupal, OSQA is a Django app, and Shapado looks pretty full-featured. There are probably more.
It'll be interesting to watch the continued evolution of the Stack Overflow ecosystem. I'm not sure any community will get the critical mass that the original Stack Overflow did, but it's worth trying a few ways to make it happen.