First, I don't understand why you're down on Samba? I use Samba in several all-linux environments. I know that M$ created SMB, but it's not a terrible protocol for what it does. There aren't too many other alternative for file sharing. And sadly, Samba / SMB is leaps and bounds above NFS in terms of security.
Second, if you are adamant about avoiding Samba, what services are you looking to offer on your network? In other words, the network cards, switches, and cabling you have between your machines is your network. So, is it that Samba offers that you want to replace?
File sharing? NFS, (S)FTP, SSHFS,
Print? CUPS, LPD
Centralised Autentication? Kerberos, LDAP, NIS (horribly unsecure), NIS+, Novel, SSH GSSAPI, SAML, etc. anything that plugs into PAM
Directory Services? LDAP, Novell, NIS, NIS+
And how about thin client computing? Why not consider not having drives in the machines themselves, and implementing something along the lines of IPv6 for the integrated encryption, XDMCP for logging into the "server", NFS for the users' home dirs, and PXE or BOOTP/TFTP for providing the stations w/ an OS image to boot.
The options are plentiful. You just kind of have to have an idea of what services you want to make available to the users, and the administrators.