Apple's strategy concerning third party applications on iOS is the target of a good deal of criticism: it's either the App Store or nothing at all. Like it or not, Microsoft will bring the same approach to Windows as it ports the platform to the ARM architecture.
Microsoft has said that Windows on ARM will not support virtualization nor the porting of applications build for the x86 platform. There are solid reasons for this, including system performance and lack of a keyboard and mouse setup in most WOA deployments. Windows and Windows Live president Steven Sinfosky mentions these issues as part of a broader discussion on WOA development.
Microsoft will tightly control the Windows-on-ARM application ecosystem. "WOA only supports running code that has been distributed through Windows Update along with the full spectrum of Windows Store applications", he writes.