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Boxes and Arrows has an interesting article on doing usability studies remotely:

Enterprise software usability is difficult to evaluate because the standard product shipped on a CD is almost always customized when it is implemented. How then can we learn about the design issues that actual users encounter with customized software?

The solution is along the lines of using WebEx/NetMeeting/VNC or whatever remote desktop viewing software you have to simply watch an end user use your software.