"majority of important software innovations have come from the open bazaar, not the cathedral. The Internet; The Web; Firefox, WebKit; GNU/Linux, Unix; HTTP; SSH, SSL, AES; Python, Ruby, C, C++."
The vast majority of those were not developed by an open bazaar, but rather by focused cathedral organizations: the early Internet, UNIX, C, C++, SSH, Firefox, SSL. The bazaar maintains them or cloned the success of others (SSH).
I also think you're vastly underestimating the influence and power over millions that continues to exist from closed commercial software: Apple iOS, IBM zOS, pOS, and DB2, SAP ERP, Oracle database, middleware, and various HR/SCM/CRM/ERP suites, Microsoft Office and Windows / IIS. The big difference is that there is an order of magnitude more revenue and more people being paid to work with commercial software than with open source.
That you claim all serious servers run Apache or Ngnix on *nix is profoundly ignorant of the millions of Windows servers and IIS servers out there, some of which power very large websites. I think Ngnix is a great server, but most of the large enterprises (banks,
Telcos, etc) I've visted in my consulting run WebSphere or IIS and have never heard of HAproxy or Ngnix.
This is not to say this is a static state of affairs. Certainly in many cases the open source alternative is a better technology or better project, sometimes even the better product. Just there's a big difference between an innovative PRODUCT and an innovative PROJECT. There are lots of the latter on Github, but other than saving people some money, they're not having anywhere the economic impact a PRODUCT has.
There is scant evidence that open source leads to more innovative products. There's a lot of evidence it helps to lower the acquisition costs of supporting software for what usually wind up as partly proprietary products. All of the latest software kings: Facebook, Twitter, Amazon, Apple, Salesforce, Google - their primary money making innovations are closed source built on (mostly non GPL) open source . Their contributions of open componentry back to the community is welcome but limited.
The only large and "purely" open company is Red Hat, and even they go through major hoops to make it inconvenient for others (eg. oracle) to use their open source code for their own purposes (ie. Offer a RHEL clone and loss lead on support). They remain innovative. But so is SAP. So is Oracle.