Below I post a script that I wrote for that purpose (my first script for Linux :D). The folder structure on my server is:
~/
~/files/
~/public_html/drupal-6.x/
The Script
today=$(date +"%Y-%m-%d")
drupal_v="6.6"
backups="files"
cd ~/
mkdir $backups/$today
clear
echo -e "TODAY: $today\n"
# 1.
echo "---Backing up Drupal 6.x without uploaded files---"
tar --create --gzip --file=$backups/$today/drupal-$drupal_v-no-files.tgz --exclude='sites/default/files' \
--directory=public_html drupal-6.x
echo -e "DONE\n"
# 2.
echo "---Backing up Drupal 6.x uploaded files---"
tar --create --gzip --file=$backups/$today/files.tgz --directory=public_html/drupal-6.x/sites/default files
echo -e "DONE\n"
#3.
echo "---Dumping the database---"
/usr/local/mysql/bin/mysqldump -u YOU -p --default-character-set=utf8 --result-file=$backups/$today/dump.sql DB
tar --create --gzip --file=$backups/$today/dump.sql.tgz --directory=$backups/$today dump.sql
echo -e "DONE\n"
#4.
echo "---Copying the settings---"
cp public_html/drupal-6.x/sites/default/settings.php public_html/drupal-6.x/.htaccess $backups/$today
echo -e "DONE\n"
#5.
echo "FINISHED. Please move the backup files to a safe location"
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