Every WebSphere Portal based application needs to handle the Session Time outs. The current solutions advocated by the Developer works usually involve usage of customization of LogOut Auth mechanism.

What I am proposing is the use of the standard J2EE mechanism of creating a HttpSessionListener. This HttpSessionListener can be weaved into the web.xml of the wps.war file ( careful as this is part of the wps.ear which is the core of the WebSphere Portal deployment). So, now whenver the session gets timed out, the listener will catch the session destroyed event and the application can handle the event.

Remember, this customization is at your own risk. IBM does not support this.
Check out the WebSphere Portal V6 Tuning Guideline here.
IBM has release a list of paper's detailing the migration steps for migrating from WP V5.1 to WP V6.1

The first paper describes the steps and best practices for migrating an existing standalone WebSphere Portal environment to a standalone WebSphere Portal V6.1 and should be followed by the majority of customers, even those in a Web Content Management environment.

The purpose of the second document is to provide a step by step guide for migrating IBM Workplace Web Content Management (WCM) version to WebSphere Portal v6.1 – Content Build for Lotus® Web Content Management (also WCM). The foundation for this document is the initial release of the V6.1 Information Center with additional information based on the outcome and experiences of our pre-release testing. With this document, we provide more comprehensive guide and highlight some of the common pitfalls and mistakes when migrating.