Perhaps the biggest new feature -- at least from a user perspective -- is the new Rollup feature that captures multiple notifications when the user is idle. Growl opens an iOS 5-style notification window that lists notifications sorted by app, keeping multiple notifications organized and contained.
Notably missing from the new version is GrowlMail, an add-on for the software that provides notifications support for AppleMail, allowing users to receive alerts about emails as they receive them. The software notoriously broke with nearly every update to Mail, and the Growl team stated that GrowlMail was more difficult to keep running than the main Growl project. The team notes that the main developer of GrowlMail, Rudy Richter, will receive ownership of it, and will continue to work on it independent of Growl.
Growl 1.3 is available on the Mac App Store for $1.99. [iTunes]