Refer to the related FAQ
Email messages are held in user mailboxes; folders located within the RcvdMsgs folder (under the WorkgroupMail data folder) that take the form usr00000001. To do a complete backup of user message data, the entire contents of the Rcvdmsgs folder should be backed up. Generally, if downloading to POP3 mail clients, these folders should only hold transient messages awaiting collection. However, if using Webmail or IMAP these folders could be quite extensive. Outgoing messages are held in the SentMsgs folder and again this folder should only hold transient messages. This folder could be included in the backup schedule.
Before backing up the message files you should consider stopping the WorkgroupMail server (see related FAQ).
In WorkgroupMail v7 we provide a free (optional) utility called the Message Archiver plug-in which keeps a copy of every sent and received e-mail message, including attachments. The messages are stored in the ArchivedTXMsgs and ArchivedRXMsgs folders under the WorkgroupMail data folder. This utility provides a first line recovery capability but no security against disk failure or accidental deletion. To achieve this you would need to incorporate these folders and their contents into the backup schedule for the server. (A scheduled script could copy the archived messages to a data drive that would be more suitable for a backup operation). To import the Message Archiver plug-in click File, Import plug-in… and browse to the file C:Program FilesWorkgroupMailmessagelog.dll
Whilst doing the backup it would also be beneficial to make a backup of all *.dat configuration files in case of corruption. These are located in the WorkgroupMail data folder. See the following FAQ