/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain user
You may need to reboot for the changes to take effect.
I think this issue has severely exacerbated since 10.8.2. Every time I update an app in the App Store it starts duplicating the apps. It's happening on ALL my 10.8 machines.