If you have several servers and want a central backup server, especially with the variety of things you have like MySQL, I personally would choose Amanda. You may want to use ZRM for MySQL (Zmanda Recovery Manager) to manage the dumps from MySQL to disk, and then use Amanda to take care of general backups, including those dumps. You can do it to disk or to tape. While you can also do it to Amazon S3, bandwidth to that would limit how much you could backup, and it would also have a cost associated with it.

Check out

Minimalist SysAdmin Blog Archive Ten Things I Like about Amanda

MySQL Backup: Zmanda Recovery Manager for MySQL

Amanda Open Source Backup

Main Page - The Open Source Backup Wiki (Amanda, MySQL Backup, BackupPC)

Both ZRM and Amanda are open source, but you can also get support contracts from Zmanda if that is the sort of thing you want.