The command line utility screencapture claims to be able to capture a single window without requiring interaction, but I can't figure out what to pass it.
-l<windowid> capture this windowsid
It's not the process id of the the application.
For some applications you can use AppleScript:
It doesn't work with Chrome though.
The IDs are also shown in Quartz Debug (available from developer.apple.com/downloads) if you run