Just used WordPress Automatic Upgrade to do an upgrade from 3.00 to 3.01, taking file and database backups. Then upgraded the Genesis theme framework which overwrote some custom files so went to the WAU backup only to find that it hadn't backed up the wp-content folder! :-(
Have been using this plugin for a couple of years with no problems because it does backups as part of the upgrade process. Disappointing to find out now the hard way that it can't be relied upon.