Do you have a second drive attached (such as a backup drive with all the apps on it)? Those have a way of making their way into the menu after a while.
You can clear out the menu with this command from the terminal:
Code:
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -r -domain local -domain system -domain user
One side effect: the warning about "this is the first time you have opened this program blah blah blah" will be reset.
The doubling will eventually come back if there are extra copies of apps around, though.