OK, I got more than 30 sites in WP running on 2.9.something version and there is a question should I update to 3.0? I'm well aware of what my brain is telling me to do - updating is always smart and useful and sometimes a must to prevent possible security issues. But I have 30+ sites and it would take a long time. My question is: how much is WP 3 going to mess up my themes and well tweaked settings from 2nd version?
Are you aware of the gaping hole in the 2.9 version? We've seen many MANY sites with code injections due to the outdated version.
Themes are always an issue as sometimes they may not work, but test it out - I've had very few themes that couldn't withstand the upgrade, and those that couldn't usually had an upgraded theme available anyway.
Going from 2.9 to 3.0 was a big change in code, and a lot of holes patched and fixed. It's definitely worth the time invested to get your site back on track and secure.
As long as your themes are not too old, they should work as is, but may not support the new things like custom menus, that comes with version 3.
This is where an auto-installer would help you out. Had you used installatron or softaculous to install these, making backups, upgrading and restore those that didn't upgrade would be a trivial matter. (Somthing to look for in a host in future).