The documentation is incorrect ( for iOS )
The call to confirm does not block, so it cannot return the value because the user has NOT chosen anything yet. The call to confirm returns a delegate, to which you can attach a callback.
The callback is 'onAlertDismissed' and will receive arguments of the index of the button the user chose and the label text displayed on the button the user chose.
Note, navigator.notification.alert returns the exact same thing, so you can know when the alert is dismissed.
This function is available in the upcoming PhoneGap 0.9.2 OR the EDGE version.
This is the correct way to call confirm:
var delegate = navigator.notification.confirm("You are the winner!","Game Over","Restart,Exit");
delegate.onAlertDismissed = function(index,label)
{
if(index == 1)
{
// user said Exit! do something appropriate
}
}