Assuming you are not running a cPanel box, the best software I have found for running backups (this also assuming you are going to keep in mind disaster recovery)is AMANDA http://www.amanda.org/ (much more reliable than manual backups) There are some issues on some linux boxes and backup failures so verify that the backup is good and restoreable. Another package I have started to try out is Mondo http://www.mondorescue.org/ I can not say much about it yet as I only have limited experience with it
If you are going to do all of this manually, you can stop Apache and tar up the home folders and then the databases. Just Google "Linux backup" and you should find a lot of accurate data for command lines. I would campaign for a solution like the above software myself.