Each application is different: It has different steps that it walks through to service a user request, it has different interactions with back-end resources, and it has a different set of business requirements that it must satisfy. For example, consider an application that handles incoming purchasing requests over the Internet from a company's trading partnersthe nature of its core transactions is to receive the incoming request, submit the request to the database, and return an acknowledgment. This is quite different from an e-commerce web site that is presenting a catalog of items for a user to purchase, maintaining a shopping cart, and processing credit card transactions.
The bottom line is that because these applications are different, they will use application server resources differently, which requires a different configuration. This is the most crucial step of the tuning process: understanding your business domain to define a set of representative transactions that accurately portray your true (or expected) end-user experience. If you do not do a good job here, you cannot expect good results once you open your doors for real-life users.