/etc/pam.d is where your main pam configuration is stored, it is essential, do not remove it. /etc/pam_smb.conf is used to configure the pam_smb_auth.so pam module that can be used to do NT4 style authentication against a Windows domain. Unless you are using pam_smb_auth.so in your pam configuration it is not needed.in my linux system,there is a directory pam.d and a file /etc/pam_smb.conf.
Barry