Microsoft basically invented the hardware-agnostic software platform. Before Microsoft, there were a variety of hardware platforms, each with their own libraries and languages... not unlike the situation today with phones. Developers had to choose what to target... not only Mac vs PC, but different video cards, different sound cards, different network stacks, etc.
Microsoft took that fragmented market and unified it under a set of standard APIs for both hardware makers and software developers to target. I would consider that an innovation: the loose coupling that they enabled allowed much faster innovation in both hardware and third-party software.
Interestingly, Netscape tried to play the same game on top of them (unifying Windows, Mac, and UNIX under one standardized API), and though Microsoft was able to destroying them, Webkit has succeeded where Netscape failed, and it is slowly making Microsoft irrelevant, just as Gates feared.
Other than that, I don't think Microsoft invented much. But they did a good job copying, were ruthless with business executation, and so their one innovation ended up being a multi-trillion dollar innovation.