Media Center has the ability to add in external programs for launching in it's programs area, there is a how-to in the Jnes help section of this site on how to do that.
Not all games support being launched from Media Center, they don't wait for it to release its full-screen exclusive mode. There is a utility included with the DirectX9 SDK called "MCE Launcher" that Microsoft provides to developers that they can distribute with their applications that provides them with an easy way to be launched by Media Center.
I've compiled this utility and provided it below, in addition there are several fixes and enhancements I've made that will be useful to you when integrating games that aren't Media Center aware.
Relaunches Media Center when you exit your game
Sets current working directory to your game's folder
quotes arguments to child processes correctly
The idea here is when you create the shortcut to the application, which is what Media Center will launch configured via your xml definition, you prefix the shortcut's command line with MCELauncher.exe
For example if your game executable and arguments are: C:\Program Files\Game\game.exe -fullscreen
Copy MCELauncher into the location and create the shortcut as follows: C:\Program Files\Game\mcelauncher.exe game.exe -fullscreen
Overall integrating applications is can be a real pain between learning the XML definition to do it, and creating these shortcuts with MCELauncher. But, once done, it's damn sweet to have the ability to launch your favorite emulators or games from Media Center from your couch.