I manage around a dozen WordPress blogs, and I've found the ability to use SVN to manage upgrading to be indispensable. I've even created a script that automatically updates all the versions by calling svn sw on each blog directory.
One thing I'd really like to see is a command line database upgrade script. Could be a shell script, could be a PHP script that just gets run on the commandline. But something I can add to my flow so I don't have to manually open /wp-admin/upgrade.php on each blog manually in my web browser.
Thanks for listening. Apologies if this has been suggested before, my Googling didn't turn up anything.