Hey, I just found out that the iPod syncs properly with NFS filesystems, so if you're using Samba (as opposed to a Windows server), you should be able to export that filesystem as NFS as well (making sure to allow connections from ports above 1023), and sync it that way. That's some seriously flaky SMB support.
Edit: Turns out that despite the fact that I allowed ports above 1023 to connect to my NFS server, it's still not working right. Works okay if I supply a `-P' option to my mount_nfs command in MacOSX, but that's a real pain. Gonna see if I can figure out how the MacOSX automounter works.
Edit again: Check out
this automount NFS doc. It worked for me. You don't really need to edit the machines NetInfo stuff unless you don't have another name service running.