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).
For Growl 1.3 (App Store) to work with Mail.app under 10.7.1, you need to install the actual GrowlMail 1.3 Update: GrowlMail1.3 does not work with Mail.app 5.1 (OS X 10.7.2), there’s a new version 1.3.1 that does work.