Just upgraded wpmu from 2.9.2 to 3.0.4. Everythning went well except for that I still got the yellow warning text at the top of the adminpage:
"The wp-content/blogs.php file is deprecated. Please remove it and update your server rewrite rules to use wp-includes/ms-files.php instead."
This shows even though I have changed the rewrite rule in htaccess as instructed.
Image uploads work fine after the update.