How to reply to comments in Android Market?
Sounds like Google has now given the ability for some developers to begin adding responses to comments within Google Play. Unfortunately, it is only to Google's "Top Developers"; hopefully, the ability will be extended to all developers soon. Read more here.
Here is the original Google link.
Update: Yes, please check Jon's and other's answer. Below is the outdated answer but you can still use some of the ideas.
There is no such function, an alternative way to do that would be adding a feedback function directly in the app and send the message via email or HTTP post back to the developer.
While implementing the feedback system, consider a thread-like conversation with a user if your project is big enough. You can even use a webview to avoid extra coding in the app and set the webview to a comment page.
It looks like this is in the pipeline, being deployed to some developers as of the time of posting: Google Play will allow Android Developers to reply to customer feedback.
Edit 16 Apr 2013: I can now reply to comments on my own app, as of several weeks ago. So either the rollout has continued steadily and recently touched me, or it's now available to everyone.