This week's giveaway is in the EJB and other Java EE Technologies forum. We're giving away four copies of EJB 3 in Action and have Debu Panda, Reza Rahman, Ryan Cuprak, and Michael Remijan on-line! See this thread for details.
The major difference is the IBM portlet API lets you define an abstract portlet application and using this via concrete portlet applications. In JSR 168 API, there is no concept for concrete portlet application. But JSR 168 API is independent across platforms.
You can choose any of the API as per your requirements.