Each application has a config backup/restore operation. ISE has a config file that contains more than just the config - it's a PGP encrypted bundle that contains many files and logs.
Prime is the same - one massive file that contains a lot of stuff (and there are two types of backups - one that contains more than just config).
Not sure about MSE - this is an ISE forum after all ;-)
Do a google search for ISE config backup. it's pretty straightforward especially when you schedule the job to run regularly.
cheers
