I haven't yet upgraded to WordPress 3.0 because a lot of my plugins aren't compatible yet. (Happily, BackWPUp was one of the earlier plugins to get a bump for 3.0 compatibility. I'm very thankful that Daniel has put in so much development time over the last week or two to push out all the new releases. :-) )
BackWPUp seems to back up fine, but there are errors on the settings page for my backup job. Specifically, the page generation dies in the "File Backup" section with a "Fatal Error: Call to undefined function
is_multisite() in /app/functions.php on line 578."
Because that function didn't exist until WP 3.0, my site (still on 2.9.2) throws an error and I can't change most of my job's settings unless I temporarily install an older version of the plugin.