Well that was simple.  Upgrading from WordPress 2.9.x to 3.0 was not such a big hassle, as long as your hosting provider allows simple cpanel DB access and rsync over SSH.

1. Backup the MySQL database through phpMyAdmin.  Check.
2. Backup the entire web filesystem using “rsync -va” (over SSH of course).  Check.
3. Click the “upgrade” button in the WordPress backend.  Check
4. Click the “upgrade database” button in the WordPress backend.  Check.

Painless!  But if you’re stuck with old-skool FTP, and you need to recursively copy your web filesystem…well, good luck with that!