This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
The WAS6.1 does provide the backward compatibility with all the versions of struts, JDK & J2EE technologies that was supported by WAS5.1.
So if you are just planning the application server migration than you can just go ahead with the straight deployment of existing EAR to new server, But if you want to migrate to latest specifications than i would rather suggest an incremental approach i.e. move from struts 1.0 to struts 1.3, JDK1.4 to 1.5 & J2EE 1.2/1.3 to 1.4.
If you are looking for the highest supported versions than please have a look of the IBM WAS6.1 tech documentations.