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The window looks a little horrible on Mac. Why can't they use Growl notifications just like other apps do?
The notifications are allowed to be full webpages - which can then communicate back to the parent window. (or extension)

This will be a reasonable alternative to modal dialogs for chrome extensions initially, and eventually for web apps in general. (if it gets adopted by other browsers)

http://www.html5rocks.com/tutorials/notifications/quick/

Anybody know how this works? Will my web-app be able to send notifications to the desktop? I assume so if it's going to be cross browser.
This works only in chrome, your web-app can also do this, but the user will have to authorize your web-apps use of this. I wrote a small chrome reminder extension which used these notifications => https://github.com/minhajuddin/quickr . That should show you how to create a notification from your app.