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.
5) Games: What about the graphical layer? Can I write the majority of my game as a Linux binary and only have the rendering bit left over to separately implement for Linux/Windows? Will this spur an increase of cross platform games?