You should back up the entire citadel/ directory (usually found in /usr/local/citadel/).
Since Citadel uses a journaling database backend, it is vitally important that you backup both the data files and the logs, and that the data files (citadel/data/cdb.*) are always backed up before the logs (citadel/data/log.*). The logs must always be backed up after the data files.
It might be apropriate to move the logfiles to another location. You can however speed this up by using LVM and snapshots.
This section of the system administration manual goes into more detail.