There's a lot of different ways to come at After Effects, and a lot of feature details to miss. One feature that slipped through the cracks here is Layer > Transform > Center in View (Com/Ctrl +Home). If you use CTL+Shift +drag almost exclusively to snap layers to the center of the comp, it's easy to miss that this command uses the Anchor Point instead.
Beyond the big list of big CS4 features found in the New features in After Effects CS4 section of After Effects CS4 Help on the Web, you can read about every CS4 change to the UI in User interface changes from After Effects CS3 to After Effects CS4. Todd Kopriva's an unordered, approximately comprehensive list of new features in After Effects CS4 covers similar ground from a slightly different perspective.