Good work – I’ve been running it without a hitch since last night.

Just a note in favor of using a version control system and staging area to mitigate problems like the one Dave mentioned above:
We have a wpmu staging area that’s also the working directory of a mercurial hg repository. We also use a custom theme in the themes/default/ folder. When we upgraded to 2.9.2 yesterday, our customized, default theme was replaced with the WordPress default theme. All of a sudden, all of our blogs had lost all of their customizations and were using the default WordPress theme.

No big deal. Since we performed the update on our staging installation first, nobody outside of our staff saw the problem, and since the staging area is a mercurial working directory, it took us about a minute to revert to WPMU 2.9.1, giving all of our blogs the correct appearance again immediately. We figured out the source of the problem, came up with a solution for it, and had WPMU 2.9.2 installed again within a matter of minutes, this time with our custom theme correctly in the default folder.

Had we not used a staging area, the problem would have been visible to the world. Had we not used a version control system, it would have taken longer to figure out the source of the problem and fix it, and the problem would have remained visible until it was fixed.

Long story short: If you’re managing a professional wpmu setup for paying customers, you should really consider making use of a staging area and a version control system 🙂