Currently notifications in unity are what they called: notifications: they don't do anything else... I really like in GS to be able to answer immediately or a friend complained that he wants to click on the notification to open the program behind.
First of all I would move the bubble closer to the panel
Then after a short delay i would "minimize" it if you click on it in this state it would open the application which is linked (in this case banshee)
If it would be a chat program and you would hover the minimized bubble it shows a text field, where you can enter a message... if you click on the bubble above the field it would open the chat window
NotifyOSD was discussed at length on this list, especially the clickable non-clickable and positioning part..
I don't know how much of the discussion ever made it into the code, but i do know that the discussion is not over yet ;)
what you are suggesting looks quite like bringing indication and notification closer together, it is an interesting idea.
how about somehow docking the bubbles to the category indicator they are related to?
Notifications that have no indicator relationship can pass as usual..