Craig Hockenberry writes about Multi-touch on the desktop:
"If you’re one of the people who think that a multi-touch monitor is a good idea, try this little experiment: touch the top and bottom of your display repeatedly for five minutes. Unless you’re able to beat the governor of California in an arm wrestling match, you’ll give up well before that time limit."
As much as I want mutlti-touch monitors, I think he's right. A little physical gesture pad would be cool though :)

I like Dominik's idea of a dual-input approach. Of course, the risk you run there is that you get into a situation where you have to manage applications on their associated screen (because one has touch input, and the other does not.)
-ch
http://www.dejal.com/blog/2007/07/multi-touch-desktop
I agree that a nearly-horizontal multi-touch surface would be the best.
http://www.ok-cancel.com/comic/3.html
For a desktop, you could have a keyboard with a nipple-style controller over on the left side. In multi-touch situations, you'd just twiddle that while you twiddle the mouse with your other hand. The computer would sense that the second control was in use, and provide multi-touch functionality.