This is the procedure for upgrading a WordPress installation. It is based on the procedure from WordPress. However, this procedure is optimized for those, who has direct shell access to their web server.
Backup the database.
Backup the WordPress directory, download and install the new version.
cp -r www.foobar.com www.foobar.com-backup
cd www.foobar.com
rm -rf *
ftp http://wordpress.org/latest.zip
unzip latest.zip
rm latest.zip
mv wordpress/* .
rmdir [...]