There is no longer a Window-based Application template starting from Xcode 4.2.
You have two other choices of "bare-bones" templates:
View-based Application template, which gives you a view on a storyboard to start with. It is similar to the one found in previous versions, except the view now resides on a storyboard which Xcode 4.2 makes use of.
Empty Application template, but you'll have to manually create and wire up a window nib file if you want to design your application in Interface Builder. It's nothing more than a trivial extra step, though.
If you can't make use of storyboards (e.g. to deploy to iOS 4 and earlier), you most likely need to go with the empty template. For the main window, just make a new Interface Builder file and assign it as your project target's Main Window.
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