Please see http://puppetlabs.com
for information about Puppet. There is a free version of Puppet and a pay-for version. I've found the free version suitable for my needs, even up to several hundred machines, assuming the puppetmaster is strong enough, but YMMV. There are other option such as Chef, CfEngine, etc.You'll have to try a few out and decide if any of them work for you.
You need to understand that NIS is a directory service like LDAP, not a domain controller in the Active Directory-esque sense of the word. The login is handled locally by the client, although it receives information from NIS. If you want a script to be run at login time, you'll need to provision each machine to do this (can be done via Puppet). If you have Automount set up, then users just need to browse to the appropriate directory to see their files.