Well for one they use parallax (on the iPhone) which obviously communicates depth, plus background items out of focus, plus there is a very very light drop shad

Well for one they use parallax (on the iPhone) which obviously communicates depth, plus background items out of focus, plus there is a very very light drop shadow on all the icons (oddly a png directly encoded directly into the html on beta.icloud.com) and a shadow around the text. The icons themselves are mostly flat with some exceptions (Contacts has a very strong bevel and there is a slight bevel on the notes icon).