Growl retains registrations because we have no reliable way to know
whether an app was deleted, or just moved. There is no general
command to do a cleanup, but you can go through the list and delete
the apps you want to that way. If its a lot of apps, you can quit
Growl, go into ~/Library/Application Support/Growl/Tickets and delete
tickets there, and then relaunch Growl (this option will go away in
Growl 2.0 when tickets will be moved into a single core data powered
database)