I used WebScarab from the OWASP project:
<http://sourceforge.net/projects/owasp/files/WebScarab>

Launch webscarab, go to tools -> credentials, then check "Ask when required".
Open Httrack, configure the proxy settings to use localhost port 8008 (the
default for webscarb) and try to mirror your intended site. If that should
fail, you can do the same with a browser, point it to webscarb
(localhost:8008), restart the browser if it's IE, go to the NTLM site,
WebScarab should prompt you for creds, input them, and you should proceed.
From then on, anything proxying through webscarab requiring those same creds
should be sent through, so you can retry Httrack if it failed. Further
authentications will prompt in WebScarab if the site prompts again.