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).

:) It is the one that you see when it is built by Apple. Says the guy who buys everything Apple produces :)

In iOS7, menu transparency that blur the content below it give a sense of depth in a similar way drop shadows do. UI elements are in the top layer, with content in the lower layer. Parallax in the home screen is also there to add depth, as well as a very subtle transparency in some app that allow you to see your (blurred) wallpaper while in app.

There are also some interesting use of solid color to indicate interactable elements (icons or links that are part of the UI are in the same solid color) that will be greyed out when there are layer above it (e.g. via action sheet).

Most of these are not in the iCloud website, however. And I'm still not sure I like the new visual style.

There are subtle gradients. Take a look at the tabs in the contacts icon. Or the (subtle) shadow under each icon.