The patent, unearthed by Redmond Pie, goes as follow:
Anyway, what this means is that different applications, or even windows within that application, can be colourised differently. This may seem annoying at first (and I'm sure lots of Windows developers will find a lot of extremely annoying uses for this technology), but it may be useful in some places. I can see how an application demanding your attention might change its colour slightly, in addition to, or replacing, the blinking taskbar entry.
Another possible use is aiding in multitasking. You could have all Firefox windows sport a slightly different colour than your Opera windows, or your Notepad windows, or whatever other application's windows, which would make it easier for some to select the right application to switch to. I'm sure others can come up with other possible uses for this patent.In fact, this patent is already more or less in use in Windows and Compiz today; unresponsive Windows turn black and white when running Aero and Compiz, indicating they might be about to die. Some Compiz plugins also allow you to opacify the parent windows of dialogue boxes, which is effectively another implementation of this patent.
Of course, this is just a patent, one of the ten billion million three-hundred ten that companies like Microsoft and Apple apply for every day, but still, it is fun to theorise over what such a user interface patent could be used for.