WebSphere application server is a Java based server and requires a Java virtual machine to run the server and applications deployed on it. Tunning underlying Java virtual machine can play a major role in tuning performance. The WebSphere Application Server runs on different JVMS. In most of the cases it is IBM JDK, but on Solaris it is Sun JDK,.. What parameters you can use and the syntax to set there values depends on the type of JVM your tuning.
The parameters that can be used for tuning JVM can be divided into following three types and you can tune all three of them from WAS Admin Console this page