You may run into problems if you're using Windows or LDAP security. I'm less familiar with LDAP, but if you're using NT or Active Directory, I'd recommend that you back up the directory structure, or at minimum, keep a list of Windows Users. If you bring up your environment without the mapped users, you run the risk of losing scheduled reports and instances.
Also, I'd recommend that you document all custom configuration (extra commands in the CCM, for example), logins (service account used by various servers) and back up all .csp files (modified for SSO, for example).
Its important to do all these things, but I'd actually recommend that you run your system db and FRS on a different server than your CE server. This way, if the CE server goes down, there's less to recover. If the File/DB server goes down, there's less to recover.
There aren't any guarantees, but if you do all of these things, you have an excellent chance of bringing your environment back up with minimal losses (typically every transaction since the last backup).
~Kurt