This is a vague guess based upon what you have written and what I would do. First, your probably not going to be able to do a straight software upgrade. Therefore, I would back up the following directories based upon default installations, etc.
/home (just in case)
/var/www (or wherever else your web application resides)
For mysql, I would login to the mysql monitor and make sure you have a listing of all your db's. Next, I would use mysqldump to output the mysql db data to a sql file. I have had success with the --opt option, please see the mysqldump man page for further options.