I looked into this a couple weeks ago, and as I see it here are your options.
1. Use mod_ntlm in apache. This handles the automatic passthrough NTLM authentication that IE performs.

2. In a Win2K AD environment, Kerberos can be used. Check out the Kerberos Authentication apache module.
I am choosing option 2, but we haven't deployed Win2K yet. As soon as we do, that will be my solutions.

After re-reading your question, I realize that I assume you are using Apache on Linux.

Dave