In the beginning there was the word, and the word was Metro. And then it was Windows 8-style. And then it was Modern. And then it was Windows Store. And then it was Universal. And today, Microsoft has decreed that henceforth these apps - which are all ultimately based on Windows Runtime - will be known as Windows apps.
Historically, of course, "Windows apps" (or "Windows programs") referred to standard, Win32-based executables that ran on the Windows desktop. Under the new naming scheme, these Win32 apps will now be called Windows desktop applications. As you can see in the slide above, despite the new nomenclature, the differences between the two types of app remain the same.