In BackupAssist 5.2.2 we introduced support for backing up Exchange 2007 via Rsync and File Replication. Instructions for how to do that are in this previous blog post. (That post only mentions Rsync, but the procedure for File Replication is the same.)
Now with BackupAssist 5.2.5 we have extended that support to Exchange 2003 as well. The steps you need to take are the same as for Exchange 2007, however there is an additional step necessary if you are running Windows Small Business Server 2003. On SBS 2003 the Exchange 2003 VSS writer is not enabled by default. To enable the VSS writer, follow these instructions.