If you are still using Skype 2.8 and switched to Growl 1.3, you need to update the Growl framework that Skype uses. Go to the Growl download page and get the Growl SDK (1.2.2 does work, at the moment there is no 1.3 version).
Open the downloaded dmg and change to the Frameworks folder. You need to copy the Growl.framework folder into your existing Skype installation (quit Skype if it’s running).
To do this, go to your Applications directory, ctrl-klick on Skype and chose „show package contents“. Then navigate into the Contents folder and replace the existing Growl.framework with the one from the Growl SDK.
Restart Skype and it should register with Growl.
[Update 12/01/2011] The Growl Version Detective, available from the Growl Download page, does this very trick for you and as well searches for other apps that use growl and might need an update.