There are two ways you can run Drupal 6.x at Stanford.
Request your Drupal 6.x site on the Stanford Sites service. This is open to everyone, including individuals. Installation is easy and code updates and maintenance are handled by IT Services. You can't install your own modules or themes, but installations come with plenty of pre-installed modules chosen by the community. Read more at sites.stanford.edu.
As of 4/10/09 IT Services offers an installer for Drupal 6.x. You can find it on tools.stanford.edu under Web Services, Collaboration Tools Installer. It's available to groups and departments, but not individuals. This tool installs a Stanford-ready version of Drupal 6.x, performing all the tweaks that used to be required manually. Once installed, you can take advantage of the Collaboration Tools Upgrade tool (recommended) for updates to core and a few installed modules, and add your own modules and themes.
To set up cron so that cleanup and indexing tasks can be run independently, see John Bickar's excellent guide: Running Cron