We previously talked about how you could now send messages directly from the Notification Center in OS X Mavericks.
This feature actually extends to incomming Messages notifications as well.
In an Messages notification in OS X Mavericks, just hit “reply”, type your message and press enter.
For this to work, you need to have notifications enabled for the Messages app. To check on this, go to System Preferences -> Notifications -> and see if Messages shows up under “In Notification Center”. The alert style needs to be either set to Banners (that go away after a while) or Alerts (that will stay on your desktop until dismissed).