Hi. One of my 4 Joomla! installations (all in my Lunarpages web space) wouldn't upgrade using Fantastico. The problem was related to a database table that had crashed; it was part of the mambowiki component I'd added to Joomla!

After a quick consult with Lunarpages support, I fixed it myself and I'm just posting the information here in case it might help someone else. Having made sure I had a good backup, I used phpmyadmin to drop the offending table. At that point the upgrade was possible. I then uninstalled the component and installed its latest version. Wonder of wonders, the rest of its data was intact, i.e. the actual wiki pages were okay.

I think that if you make sure you have backups first (preferably including one from before a problem came up) you should not be too worried about doing whatever it takes to make this stuff work. Of course, if you can keep a copy of your whole site somewhere, and always test stuff on the offline copy first, that's even better, but many of us just don't have the time or patience to do that. So, when in doubt, go for it!