It looks like Pantheon, the elementary OS DE will be getting a new notification daemon called Pantheon Notify which supports several notifications at once, it expands on hover if the text is too long to be displayed in a regular notification and it supports closing the notifications.
Here's a video I've recorded with the latest Pantheon Notify version in action:
(direct video link)
Pantheon Notify isn't ready to replace Ubuntu's Notify-OSD just yet - for instance, it doesn't support displaying notifications when changing the sound volume or notifications that use HTML (which is displayed as plain text in Pantheon Notify), but these issues shouldn't be too hard to fix.
Pantheon Notify is available for testing in the elementary OS daily PPA, for Ubuntu 12.04 Precise Pangolin (and, obviously, elementary OS Luna). To try it, you'll have to "kill" notify-osd, then run "pantheon-notify".
What do you think?