I've been documenting my discoveries in WAS 6. One issue is performance: Everyone wants it. How do you get it?
The WAS InfoCenter has a page dedicated to this topic: Performance: Resources for learning. One particularly noteworthy resource is "WebSphere Application Server Development Best Practices for Performance and Scalability" (PDF) by IBM's Harvey Gunther. It's a bit old (Sept 2000), but organized around basic practices (patterns?) that are still applicable today.
Another resource is WebSphere Application Server V6: Scalability and Performance Handbook (draft), one of the WebSphere Redbooks. Among other topics, ISSW's Robert Peterson discusses how the default messaging JMS provider in WAS 6 is actually super fast (even though Java is supposedly slow); see the comment on RAD 6: Listener Port vs. Activation Spec (Part 2).
Keep in mind a cardinal rule of performance tuning: The app has to work right, then fast. Performance optimizations that may sometimes cause incorrect application behavior or data corruption are detrimental, not advantageous, and need to be avoided. See Developing Code: Make it fast, which assumes that the code already works correctly and is written well. Problem with Service Locator Pattern shows what can go wrong.
Remember: If a performance optimization breaks the business logic, then all you've got is an application that fails really fast.