I find it amazing that you can have such a functional Ubuntu environment by translating system calls. Microsoft does have the advantage of Linux being open-source I suppose, while the Wine project had to reverse engineer DLLs. Or have you supply them on your own.
1) Linux has won the server (web) market. Developers would like to use a Unix box to work on their server code so they typically move to OS X. This could prevent that switch because they can still use Windows to developer their Linux server software.
2) Many projects start out as Linux and stay Linux and are only ported after much time and effort to Windows. Enterprises when faced with a tool that they want to use will also look to switch off Windows. Now rather than the cost of switching they only have to pay to upgrade their windows boxes to use the tool.
3) There is now a major incentive for developers to only build Linux binaries because it will work more places. This might cause a faster drain of developers as they eventually remove all windows specific code and can more easily migrate elsewhere. This feels eerily similar to the OS2 story and no doubt in the next week I expect to see more than a few articles discussing this very thing.
4) It will be much easier for Microsoft to bring much loved Linux tools to Windows so you can expect to see a more rapid increase of tools announced that now work for Windows.
Although, as others have already pointed out, it differs in some very significant ways.
OS/2 2.x providing Win16 binary compatibility was an after-market system providing binary compatibility with applications made for the operating system that shipped "out of the box". Whereas this is the operating system that ships "out of the box" providing binary compatibility with applications made for an after-market operating system.
(Yes, yes. One could buy OS/2 pre-installed, and one can buy Ubuntu Linux pre-installed. The scale of that, in both cases, is nowhere near significant enough to change the basic fact that overall the two situations are the reverse of each other.)
Also: There was not the extent of existing tools available natively on both platforms, in the OS/2 case. The examples being waved around in the news now are things like Apache, Ruby, Node, and so forth. There wasn't the OS/2-and-Win16 analogue of (say) the Ruby developers deciding in the months to come that a Win32 port is too hard to maintain, and dropping it in favour of just running the Linux Ruby on the Windows NT Linux subsystem. Today's analogue of the OS/2 case would be a universe where there was no Win32 Ruby at all, and the Ruby developers deciding not to start making a Win32 version because the Linux one "is good enough for the few Windows users".
I suspect that drawing parallels based upon what happened with OS/2 2.x and Win16 is a mistake, and those thinking that this will mean an outflux of Windows development "because it happened with OS/2 2.x" (which was more like an influx of development that failed to happen) are indulging in wishful thinking.
There's also the minor matter that, during the OS/2 2.x and Win16 time, there was this little thing called Windows NT lying around, promising a route for OS/2 1.x, where the existing tools were, with its OS/2 subsystem. (It is ironic that we are once again looking at a Windows NT subsystem.) That has no equivalent this time around at all; unless one mis-casts UbuntuBSD (https://news.ycombinator.com/item?id=11326457) in that rôle. It doesn't really fit, though. "Look, all you people with Ubuntu Linux application softwares. Forget that minority Windows thing that you ported to a couple of years ago. Come bring your applications to this new FreeBSD instead." (-: