We have a subnet shared by two domains which has its own DNS servers. Forward lookup zone does not have a problem because the workstations will go and register itself on its respective DNS server. I have problem in setting up the reverse lookup zone. How do I setup the reverse lookup zone so that I can nslookup on any addresses from any domain and I get the correct reply back.
From what I understand about your request, you want to have a delegation for in-addr.arpa resolution (reverse lookups) at a sub-class level. You might take a look at this document describing the process in some detail or refer to RFC 2317 which describes the IETF best current practice on this topic.
The trouble with your Windows domains would be that you probably let your clients (or DHCP servers) update the reverse lookup zones on your DNS servers - these update mechanisms are unaware of any eventual classless delegation setups and cannot be configured to function correctly in these environments. If you need this, you probably will have to script your DNS servers to "copy" the PTR records within the zone to your CIDR-delegated zone. You can do this using either dnscmd, the "DnsShell" powershell module or the DNS WMI provider.
Take a look here. It explains how to configure a reverse DNS zone on Windows Server.
Also, you need to ask your upstream provider the delegation of the reverse DNS lookup zone for your subnet.