Software certification's actually something Microsoft have been doing since at least Windows XP, as a means of ensuring certain applications reach a quality and compatibility standard across the OS. It's not clear which certification Microsoft would like to slap on Minecraft, or how doing so would possibly benefit Minecraft, but here's a list of certification requirements for a typical Windows 8 desktop app. It stipulates 52 requirements to meet Windows 8 certification, mostly rules that ensure your software isn't crappy, doesn't restart the system, works with 64-bit Windows and plays nice with multiple logins.
It isn't compulsory, nor is it necessary.
So, come Windows 8 Minecraft will be rogue software, an uncertified bison: bold, proud, unpredictable, roaming the digital plains, potentially incapable of supporting multi-user Windows 8 sessions or following User Account Control guidelines. Notch has put everybody at risk with his dangerously uncertified code. This is Mad Max. This is the Wild West.