For Server 2008, the built in Windows Backup app will backup an entire volume and restore it to another location.
Server 2003 doesn't have this capability built in. There are many 3rd party apps that can do this also, Acronis and StorageCraft have worked well for me. Search for "image backup" for other options.
I believe that dd is the utility for this in the Linux world. You will need exclusive access to the source and target drives from Linux to accomplish this.
For just migrating the share configurations there is the MS File Server Migration Tool:.
DFS can be used if the shares will move from 1 server to a new server: set up DFS on source, configuring DFS on the target, let it replicate and then remove DFS on the source. DFS can be removed or left on the target when replication has completed.
NTFS permissions (separate from Share permissions) and printers can be migrating using other tools, Xcacls.exe / Xcalcs.vbs, robocopy, MS Print Migrator.