.NET has been very popular since its initial release. I saw it used frequently in applications, particularly when a simple form-like interface is required. It was easy to develop and accessible from several languages, such as C++, C#, and VB.NET. Enterprise application developers were particularly interested in it, especially with its managed security.
The framework drove an open source movement to write their own version, Mono, spearheaded by Novell. Some time later, the company Xamarin was created from the original Mono development team and maintains the project to this day. In fact, Miguel de Icaza was at Build 2014 discussing the initiative. He seems content with Microsoft's new Roslyn compiler and the working relationship between the two companies as a whole.
WinJS is released under the very permissive Apache 2.0 license. Other code, such as Windows Phone Toolkit, are released under other licenses, such as the Microsoft Public License (Ms-PL). Pay attention to any given project's license. It would not be wise to assume. Still, it sounds like a good step.