A new version of your operating system just got released and you want to have a fresh new install, or you want to migrate all of your data to another machine. There are so much stuff to backup that you don't even know where to start?
I will try to list the most common stuff (on a web-server) to backup or copy somewhere when you want to do a server migration.

This tutorial is targeted to Ubuntu systems, but can easily apply to Debian or other distributions.

Please also note that this should only be used as a guide, I do not guarantee that this will save all of your configuration. NO WARRANTY !

• First, make sure you execute each command as root, or use sudo.
• Make a secret temporary folder to store your backup and cd into it:

  cd "$(mktemp -d)"

• The /home folder: just tar everything, as root type:

  tar --preserve -cvjf home.tar.bz2 /home

• Backup /root

  tar --preserve -cvjf root.tar.bz2 /root

• Backup users, passwords and groups:
  • users are in /etc/passwd and /etc/shadow
  • groups are in /etc/group and /etc/gshadow,

  JUST take the lines containing users/groups that YOU created (usually they have a uid >= 1000)!

• Backup crontabs, and atjobs:

  tar --preserve -cvjf etc_crontab.tar.bz2 /etc/crontab
  tar --preserve -cvjf spool_crontabs.tar.bz2 /var/spool/cron/crontabs/
  tar --preserve -cvjf spool_atjobs.tar.bz2 /var/spool/cron/atjobs/

• Backup users' email:

  tar --preserve -cvjf email.tar.bz2 /var/mail/

• Websites:

  tar --preserve -cvjf www.tar.bz2 /var/www/

• Backup needed config files in /etc/:
  • Apache2 vhosts:

    tar --preserve -cvjf vhosts.tar.bz2 /etc/apache2/sites-available/

  • Networking configuration:

    tar --preserve -cvjf network.tar.bz2 /etc/network/interfaces /etc/hosts*

  • Postfix configuration:

    tar -cvjf postfix.tar.bz2 /etc/postfix/*.cf

  • Anything else you see in /etc/ and you wish to keep...
• Backup MySQL databases, users and privileges:

  mysqldump -uroot -p --databases mydb1 somedb2 anotherdb3 > db.sql
  mysqldump -nt -uroot -p -w"User NOT LIKE 'root' AND User NOT LIKE 'debian%'" mysql user db > users_privs.sql

I'm sure you can figure out where to put everything back on the destination server.