Our buddy Pete went and wrote up a very detailed post on how to upgrade from WPMU to WordPress 3.0 if you are brave enough right now to try out the beta2. Pete steps through it manually, so be prepared for that. (and backup your site first).
These instructions will still be relevant for the final release. The only difference is when the release is final, you will get an upgrade notice.
Thanks, Pete! Writing that post was on my list.
(Did you get the part about backing up first?)