To set up the JAVA_HOME environment variable add something like this to the global or user specific profile file. I used /etc/profile:
JAVA_HOME=/opt/IBMJava2-13
export JAVA_HOME
PATH=$PATH:$JAVA_HOME/bin
export PATH
Tomcat has its own initialization file but it's still a good idea to create those environment variables. After you set those up you should be able to simply execute java from the command-line and see the usage of the java command without error messages.
I personally prefer IBM's virtual machine to Sun's virtual machine since it seems to have fewer bugs.