DBIx::Copy allows for duplicating a database, with a little cleverness you can create backup and restore utilities using it.

The main advantage I see of using DBIx::Copy vs. a file based backup, is access rights might not allow you to write utilities to read the "raw" database files or you might not have shell access.

What SQL engine you use may also determine what method(s) are available/best. Newer versions of MySQL include replication utilites/support.