There is a problem of logging if you run multiple web application at single JVM, you can take a look here to learn more about this.

http://www.indicthreads.com/articles/406/logging_java_logmanager_shared_hosting.html

In our own expeerience, logging is not the major problem, it is easy to write a logging library. The main problem is updating individual application instance without affecting the other application instance. Finally we run individual tomcat for every application we host, which spend a lot more memory :-(