I've been documenting my discoveries in WAS 6. Along the same lines, there's a good article now on developerWorks, "A quick guide for migrating to IBM WebSphere Application Server V6."
If the title didn't tip you off, the article is about migrating your J2EE apps from previous versions of WAS--V4 and V5--to V6. The authors are a couple of IBM's WAS testers in charge of making sure that migration works, so they should know what they're talking about. The article talks about how to use the migration wizard and the migration command line tools, how to migrate a V4 multi-node or V5 cell to a V6 cell, and even how to rollback to V5 if need be.
Also check out the WebSphere Application Server V6 Migration Guide (SG24-6369-00), one of the WebSphere Redbooks. Two of it's co-authors are ISSW's own migration expert Wayne Beaton and ISSW honorary member Tom Alcott.