Yesterday, I have my first chance to use the softwareupdate command line tool. I didn't want to use VNC to run Software Update on the Mac mini. The softwareupdate command line tool allows you to do everything that you can from the UI. (This was added after I left Apple, after working on Software Update.)
One problem is that some of the installers are not written well. If you run an update for iTunes, while iTunes is running, a dialog appears informing you that iTunes needs to be quit. Unfortunately, this also appears when running this from the command line tool. This script should be changed to present the prompt on what ever interface launched the update.