Comment 12 for bug 546650

I too am affected by this bug, and does make interaction with notify-osd and Ubuntu in general somewhat counter intuitive as notification bubbles often cover window controls (of maximised windows specifically) and other UI elements.

I would suggest however that implementation of click-through, while elegant is not a long term solution, as it precludes direct user interaction with notifications. For example it would be impossible, so far as I can see, to click on a new mail notification and open up said e-mail(s) in the default e-mail client or webmail provider. A more long term solution might be to implement a default user interaction (perhaps middle mouse button) to close the notification bubble. I admit that is not as elegant as click-through, but it does allow for future developments in notification user interactions.

Lee.