The Wintel alliance looks in danger of dying according to an article by Theo Valich.
Theo says that the breakup may center on the Xbox 360 and the introduction of AMD's x86-64 instruction set. But that Intel's new Moblin V2 it will finally enter Microsoft's territory; software.
So does this mean that Microsoft is in trouble? Not really if anything they have moved on to other partners. Although the loss of the friendly alliance with Intel will be a pain it is not going to do major damage.
MS has a few new projects on the table with new partner nVidia.