Most of the configurations in citrix metaframe server are backupped by scripts or normal backups. Like published applications which you can export and import with pat.exe.

A great want to have however was the ability to backup the policies. Now recently a post on Brian Madden his website was posted that Mark Elliot has written a script to backup these policies. I for sure know that a huge number of people are Mark for ever thankfull.

Here is the article