Innovation in this context means dramatic enhancements or unprecedented class of hardware/software offerings as IT products/services evolve.
There is Mac, iPod, iPhone and iPad from Apple.
David Wheeler may have a bone to pick with Microsoft innovations but that is entirely his own opinion. In fairness, I can think of only one innovation from M$ and that is Kinect.
Those are from commercial vendors. Sure there are a lot of partners and players in the Microsoft ecosystem but their output is primarily profit-driven, not innovations of the creative type.
Truth be told, innovation is a very subjective term that its meaning is vastly biased to every individual.
On the other hand, let’s take a look at open source front:
From open source-based vendors, we have Red Hat Enterprise Linux. From pure open source CS innovations, we have MapReduce from Google, Fractal Tree from Tokutek, KSplice from MIT, rsync from Andrew Tridgell, Xen from University of Cambridge, KVM from Qumranet and a lot more.
Innovation is basically an idea, a principle, a theory.
Open source software is an implementation of an idea, a theory applied in practice.
Ideas coming from commercial vendors are trade secrets, patents, intellectual property. Ideas in the open are being contributed to ever increasing banks of knowledge.
Ideas want to be free but only if you adhere to open source philosophy.