I've released version 0.2 which adds a --fullscreen option to detect when something is running full-screen and automatically reduce intensity. From the README:
If the --fullscreen option is specified, then the pixel at location x, y is checked when the program starts. Note that 0,0 is the top-left corner of the screen, and 1679, 1049 will be the bottom-right corner if you're running a 1680x1050 monitor. This pixel will be checked on every poll cycle, and if it is different from the value it was when CGMinerManager was launched, then the intensity will be adjusted to the value specified on the command line. Note that throttling by running application takes priority, so if the full-screen app intensity is set to 12, but you're running MyApp.exe with a "-t MyApp.exe 13" command line, then the intensity will be set to 13.
On my 1680x1050 screen, I use "-fs 12 0 1049" which makes it check the pixel in the far bottom-left corner. It will normally be part of the task bar and will be a grey color (I use the Windows Classic theme in Win7), but when I'm running a full-screen program, it will be colored something else from the program, be it a game or a video. When this happens, cgminer's intensity will get reduced to 12, giving that program more GPU time.