IBM and Apple may seem to be the unlikeliest of partners at first, but the relationship truly is mutually beneficial – highlighting individual strengths (Apple – devices and ecosystem, IBM – enterprise capabilities and services) while avoiding competition (IBM is out of the device business, Apple is not particularly strong in the enterprise). This would not have been possible with IBM and Microsoft (both are competing in the enterprise market) or Apple and Microsoft (both are competing in mobile market). So, on the surface it appears to be a very important deal for the enterprise customers. It is also a deal that needs to be watched carefully as things develop (a somewhat similar arrangement between IBM and Palm did not generate much success). Read more on this subject here - Why the Apple-IBM deal matters
How does this impact Microsoft? To a degree, though I don't think the impact is going to be very profound (something I can't say about other enterprise mobility players, such as Blackberry). Microsoft just needs to be patient and persistent. I think that Microsoft is uniquely positioned for growth – with proven capabilities across both services and devices, strong enterprise presence, renewed focus on innovation, leaner operations, and more than enough capital to support its ambitions.