I'll start the response with some opinions. I'm sure others will have different opinions.
The biggest factor is what your server is. If it's a windows box, then you will probably use SMB/CIFS. If your server is *nix, then you have the choice between NFS and samba. IMO, setting up NFS is easier than samba. If your server is an appliance (NAS) you may or may not have a choice.
NFS is reportedly usually a little faster than samba. Not enough to really matter until you start to saturate your gigabit network.
Your file servers should be on your internal network, so security shouldn't be a main issue, but if it is, then there are different security issues between NFS and SMB/CIFS.
FYI, I run a MS-free house, so chose NFS servers.