Xcode 4 no longer provides any UI – that I can find, anyway – for changing the default organisation name, whether globally or in a particular project. It’s claimed that it’ll still respect the user defaults setting, which may well be true, but what if you’ve already created your project?
Well, the only workaround I can find is to open the pbproj file in TextEdit, find the offending ORGANIZATIONNAME setting, and change it to what I actually want.