Can I have an independant JVM start for each EAR or WAR file that I deploy? How is it done?
No. Strictly speaking you cannot have a separate JVM per application. Not unless you start a seperate JBoss service per application.
A J2EE application requires a J2EE run-time environment to operate. This environment consists of the JVM and the JBoss microkernel. The analogy would be wanting a different OS for each running C++ application.