I've found that WebDriver works with IE 9 and Windows / NTLM authentication via using Windows Impersonation and IE's automatic logon feature. An example of the impersonateValidUser method you'll need to call can be found here:

 http://support.microsoft.com/kb/306158 ("Impersonate a Specific User in Code")

Essentially you want to do the following (ensuring that IE 9 is configured to "Log me in automatically"):

impersonateValidUser("DifferentUser", "DOMAIN", "Password");

// WebDriver now logged in as "DifferentUser"

IWebDriver webDriver = new InternetExplorerDriver();

To revert back to the user running the tests / Selenium RC just call:

undoImpersonation();

I've found that WebDriver works with IE 9 and Windows / NTLM authentication via using Windows Impersonation and IE's automatic logon feature.
An example of the impersonateValidUser method you'll need to call can be found here:  Impersonate a Specific User in Code.

Essentially you want to do the following (ensuring that IE 9 is configured to "Log me in automatically"):

impersonateValidUser("DifferentUser", "DOMAIN", "Password");
// WebDriver now logged in as "DifferentUser"
IWebDriver webDriver = new InternetExplorerDriver();

To revert back to the user running the tests / Selenium RC just call:

undoImpersonation();