That case never made it past the trial court, and ended in an out-of-court settlement in which Microsoft paid a paltry sum to make the problem go away, setting no legal precedent. Furthermore, the surrounding circumstances included an injunction from a Dutch court against Lindows.
The term "Windows" to refer to the GUI element was in common use from the 70s (the term WIMP was coined in 1980) long before Microsoft Windows was released.
Apple Computer vs Apple Corps (music) "co-existed" (I know of the lawsuits and agreements) at the time because one was an electronics manufacturer, and the other a record label.
Paper (53) is a drawing app, Paper (FB) is a news/FB wall magazine. Completely different markets. They should be able to co-exist.
The point isn't that they are from two different categories. The point is taht both of them are iOS apps! So the case exists.
As for Apple Computer and Apple Corps, obviously Apple never tried to be a Record label company. But when it started moving its operations into the music industry (i imagine that was the itunes time?) it got attacked by Apple corps. Before that it was peaceful co-existence. After that, it was Apple computer paying Apple Corps to keep its mouth shut and not bitch about it
The argument that it's an "app" its like saying a company that has a "website", or a company that uses the "telephone" can't share the same name. The app, like the website or telephone is the medium to the service/product.