WAS CE (Community Edition) is build upon Apache Geronimo. Now, IBM has released a red book on how to migrate the applications developed fro WAS CE ed to WAS V6.1 ed. It seems all along that was the plan - get you hooked on the free stuff and once hooked, you need to move up the ladder (WAS V6.1 in this case)and start the pay back time.
Overall, the migration steps are pretty straightforward. I like the chapter 3 and 5. Chapter deals with Migration Strategy. The same guidelines are applicable for any migrations. Chapter 5 deals about Common Migration Issues - which is kind of best practices when doing such things.
Check out the red book here.