NAT with linux or windows

I am working on a project which deals with overcoming the drawback of NAT i.e. trying to run NAT-dependent services along with NAT.
One way that i could figure out was to go till application layer and change the private IP into public IP.
Now, there exists NAT functionality in Win 2003 Server. And I would write the program of changing the private IP to public IP in the application layer in Java.
The thing that i want to know whether it would be possible to integrate my program along with NAT functionality of Win Server. And if yes then how can it be done?

Or else Unix would be better alternative