Notifications stopped working for Messages (Mavericks)
The issue might be the way that you have your notifications for Messages set. If you go under Notifications -> Messages, you will see something that says "Messages alert style:" and will have the option to select None, Banners, or Alerts.

Make sure you don't have "None" set as your alert style. You can also set the badge counter to show for when you get a new message by clicking the "Badge app icon" option lower on the screen.