Application-wise, just backup NMSROOT (e.g. C:\PROGRA~1\CSCOpx). To get the dynamic stuff, you will also need a full Windows Registry backup as well.
Typically, when customers ask about FULL LMS server backups we recommend they first do an LMS data backup using the Common Services > Server > Admin > Backup interface. Then, take the backup directory and back that up to your archive server. Then do a full server backup (i.e. file system backup).
On a restore, first restore your full server backup. Then, use the LMS NMSROOT/bin/restorebackup.pl script to restore the LMS data backup you took. This will ensure database integrity.