Conducting a Unix Desktop Usability Study?

cyclop asks: "I am a close friend of a Ph.D. student on human interface usability. She's now working to tailor a KDE-vs-Gnome usability study (a pretty hot topic these days), and I have been called to help, as a long time GNU/Linux desktop user. What kind of advice -- both technical and theoretical -- would you give us on conducting a deep and objective study on the Unix desktop, that can be useful for the developers and the OSS community?" "She has installed GNU/Linux and used both KDE and Gnome to get to know them, while I provided her a number of links on background information and previous usability studies on both DE, and advised her to subscribe to relevant mailing lists of both projects. However, I feel that it's not enough and that there are a lot of potential pitfalls and misconceptions that wait for us, me being a geek and she being a Linux newbie. Moreover, she found that most of the previous studies on the web were quite sloppy, in comparison with common usability research standards."