SMS Popup or Handcent SMS will do that for you. Handsent has ALOT more features than the default Messaging app and it does the same thing as SMS Popup. So if you want to continue to use the stock Messaging app but want the popup, use SMS Popup. If you want to be able to customize your messages alot, use Handcent SMS.
I just installed Home++ and already was using Handcent. When I receive a message, there's a pop-up in the screen with the message, and option to close or reply. Nice.