1) The real question is: "is the JVM certified to run under VMWare?" At one point the answer to this question was "no," but I don't know what the status is now. (It might just be that if you need to report a JVM issue to Sun that they want you to duplicate it on hardware.) I have been running JBoss AS under VMWare for some time, and I know of many others who are doing the same (even in production).
2) Java is "compile once run anywhere." No code or configuration changes are required.