First of all, let's dismiss this false notion that Apple somehow "invented" the word "app." Here's a
2005 post in MacWorld referring to individual programs in the iWork suite as "apps." Wiktionary has a
whole list of uses of the word "app" to mean "application" prior to Apple's introduction of the App Store. The word "app" meant "application" way before the iPhone was even cooking inside Apple HQ.
So, in light of this, it doesn't
matter how other platforms refer to their software - they're still
apps, because that's what the word
means.
Now let's tackle the issue of Microsoft's alleged "hypocrisy" here. Sure, pretty much every desktop operating system has windows - but windows are one small element of a pretty huge picture. You wouldn't describe Windows (or Mac OS X, or any Linux distribution, etc.) as a "window" or "windows," would you? Of course not. You'd refer to it as an operating system.
On the other hand, how would you describe the App Store? It's an "app store" - its name describes exactly what it is. An "app" is an application, and a "store" is a place where you sell things. It's as if someone named their car dealership "Car Dealership" and then tried to trademark the term - there's no creative license being applied, they are just using an generic description as an actual name.
As far as hypocrisy goes, if Microsoft were selling actual windows you could make the argument that "Windows" is a generic term in that context and shouldn't be allowed as a trademark. But they're not - there's a layer of abstraction there that isn't present in Apple's attempt to trademark the term "App Store."
So in light of all that, in the contexts in which the names are used, which is more generic: "Windows" or "App Store?" The answer is clearly and unequivocably "App Store."