Okay, before anything else, since you want this on some windows and not others, we would need a way of knowing which windows knew how to go to the notification area. This would be done with a new EWMH property on those windows. This would mean we had to update the EWMH, which can't be done without discussion on the wm-spec-list. So that should be your first port of call.
After that we'd need a way of telling a window to notificationify itself. Then we'd need to modify at least metacity and kwin and compiz to support the new functionality and the new theme formats which the extra button would require. Then we'd need to find some way of getting themes available that used the new button. But we can talk about all that on the list, so what you should do next is join that list and ask there, giving a reference to this bug report.
(Apart from all this, I still don't see how an action which means "hide the main window and put things in the notification area" is functionally different from the action which already exists which means "hide the main window and change the status in the task bar", or that you've explained this anywhere. But again, we can talk about this on the list.)