I think the answer to a "third place" is to create glue that enables users at the account level to connect with each other, but abstract away specific communication technologies and let users choose what they want.
For me the biggest challenge is how to get in touch with the SO userbase about items of discussion. The people who know each other have already found their own channels and means. But how do I even start an intention to connect with 'BigEasy5' about my answer on "C# references"? Right now I'll have to visit his profile, see a website link (if he provided it), visit the web site, and try to track down an email or something about him. Or I'll have to leave a public comment and cause comment spam.
The challenge in my view isn't finding an existing technology to communicate with, or creating a new techology which may or may not fly (although it would tightly bind the userbase to communication with one another) but how to connect within the community.
I suggest making users available to each other for communication as the first item, based on their own communication prefs, and subject to appropriate privacy controls and such.
Secondly focus on technologies that can enable that communication. Let the users choose their own way as they do now. One of the choices might be your handy dandy new "third place" web 3.5 chatroom -- think Wave killer :). Or I might choose IRC with SO users to get away from yet another web-based communication forum and log my own chatter.
I say consider separating the concepts of enabling communication and communication itself.
My answer misses the point of gathering all discussion in one place but there's already a lot of that given main and meta. I'm addressing the realtime discussion scenarios with fellow users.