There are tons of things changed between version 8.2 and 9.0. The compiler and library change alone can break tons of compatibilities. Added with X Desktop change (kde2 to kde3 and gnome1.4 to gnome2) and you can receive tons of problems in upgrading, even for package only upgrading.
So like Afrosheen said, better keep your /home in separate partition, backup the data you know you'll need (such as /var/www/html and your sql directory) and clean install from scratch, restore the needed files, and voila.. a brand new, clean, sparkling, and hassle free linux environment.