If you're hosting the sites spread out on servers all over the place, there's not much you can do.
If not, you can reduce the hassle by serving up multiple domains on WPMU.
Sadly, since the WP/WPMU merge, serving multiple domains is a bit of a hassle, but it can be done.
You can also use symlinks to use one codebase to serve as many sites as you want, so if there are no DB changes, it's just one update.
Drupal is, by the way, a lot worse UNLESS you use drush + either rysnc or cvs. Then it's quick via command line.
I don't dare to live this dangerously, but if I had as many sites as you guys do, I would just script the updates.
I'm not sure you can do it on WP, but with drupal, you can do almost any management task from the bash shell using the tools I mentioned above... and it's dead easy to run many sites from one codebase, but only makes sense if you have a very defined module set and the sites are similar in terms of functionality (otherwise you get into the situation where you want to upgrade, but site one needs version 1.1 of a module and site 2 needs version 1.2 of a module and and and).