Joined to chime in on this. It is a much-needed feature for the mac version, as most HIG-compliant applications on OS X work this way, and it is a very important user expectation. Unfortunately, windows is the opposite. Linux is a wildcard, and I can't speak for it...
As a template, the activation should behave as it does when using the built-in textedit application. double-clicks work on an inactive window, single clicks activate the window.
I'd like to say all Apple apps behave, but finder has non-compliant behavior in the application view (it allows click-through, possibly for windows converts?).
Further (and slightly older) reading : http://daringfireball.net/2003/05/much_ ... ickthrough
Thanks for the great software!