First we had Metro apps and desktops apps in Windows 8, but then the Metro name had to disappear due to the potential legal issues with a German company. Microsoft urged its employees to rebrand Metro to "Windows 8" apps and now the software giant adds to the confusing by introducing two new terms: Modern Apps and Windows Store Apps.
Neowin spoke with Soma Somasegar, corporate vice president of Microsoft's Developer Division, and received an explanation about the concept behind these two new app classes.
Basically, an application that only runs inside Windows 8's new Start screen (aka Metro) is considered a Windows Store App. A Modern App on the other hand is a high level look at applications, it does not refer to a single application but to the shell that some Windows Store apps reside in.
According to Soma, any application that spans multiple connected (Microsoft) platforms such as Windows 8 and Windows Phone, or Windows Phone and Azure, or Windows 8 and Azure, is considered a modern application. A Windows Store App can be a Modern App too, but not all Windows Store Apps are Modern Apps.
Guess we have Microsoft's marketing department to thank for introducing all these new (and confusing) terms.