Vivek,
The SAP Agentry applications were all updated to use the newer JCo 3 libaries and APIs but the underlying connection should be basically the same using the new JCo 3 methods. You will probably need to dig into the JCo 3 apis to understand what the new process / equivalent is to what you are doing today with JCo 2. Unfortunately I am not a JCo expert but maybe there is another group/area on SCN that might know more.
--Bill