I've found the colour theme settings for Visual Studio 2012 at HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\11.0_Config\Themes
I can duplicate a dark output window in the light scheme by copying the relevant key so this is definitely where the color comes from (you have to restart the IDE in-between changes).
I'm wondering if anyone is familiar with the format of the binary data in these keys?
Or the Common7\IDE\CommonExtensions\ShellColors.pkgdef file that they seem to be created from?
I've tried some experimentation with changing what I guess should be the colour values with without much success.