Anyone correct me if I'm wrong but I believe ALL of the settings are stored in the database. So you could just do a "mysqldump".
mysqldump -h -u -p >
The -p tells it to prompt you for a password, you'll need that handy as well.
This will store your database in a file that will be able to be read if you want to import your database again using this file.
Then for the files (if you've modded any of them) you'll just need to back them up manually via FTP or whatever means you have.