This developerWorks® article on tuning WebSphere® Application Server is a valuable reference: Case study: Tuning WebSphere Application Server V7 and V8 for performance
Various suggestions for WebSphere Application Server settings are also embedded in various topics when they apply to a particular task.
The Jazz.net Deployment Wiki has a section on Performance Troubleshooting
The topic Configure LQE properties contains suggestions for improving the performance of LQE.