From the User Experience documentation for Apple Developers:
You should not use a brushed metal window if your application: Is a multi-window application for example, Interface Builder Is a document-based application - for example, TextEdit Use the brushed metal window look for the primary application window and other windows that meet the above criteria - for example, the Equalizer window in iTunes. Don't use it for supporting windows, such as preferences and other dialogs. It is acceptable to have a mix of standard Aqua windows and brushed metal windows within an application, as the Finder does.
Now I know why my mac doesn't have a way to change the skin of all apps globally. XP has this figured out pretty well and gives itself a uniform look across. In OSX I have to deal with each app and each window in each app having it's own set of skins, brushed metal, round corners, square corners, and burnt metal now with the new iTunes. Sure I guess It's great that I can tell mail from safari by seeing a different skin. But really I hope to see per application skin support built natively into all tiger apps going forward, as there is currently for language support. Can you imagine if each app was forced to a specific language?