"The Matrix: Reloaded" does it right. Trinity's power grid hack shows her using the free Nmap utility to sucessfully gain root. Nmaps author, Fyodor, noticed the sequence and had this to say:
"All was going well, until Trinity needed to do some hacking," Fyodor wrote to CNET News.com in an e-mail interview. "This always ruins movies for me, as they almost always pass off ridiculous 3D animated eye-candy scenes as hacking. But then Trinity pulled out my Nmap program and did it right! I was so shocked that I almost did the 'r00t dance' right there in the theater!"