In my experience, WebSphere 5.1 applications port quite easily to 6.1. Naturally, it depends on how complex your applications are and which features they use. I'd suggest you take a look at the Migration guide.
I saw the Migration Wizard book. It's very helpful to me. But my current version of WAS 5.1 is running on Linux. I want to put WAS V6.1 on Windows. Is this possible through Migration wizard ?? Bcoz we have to give the path of existing server home directory while doing the Migration Process.