I just installed Java 1.6_07 so I could try profiling with VisualVM. It tells me that my app is spending 60% of its time in sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run
How do I find out what it was doing during that time? How much of the time was it waiting for something to call it, or doing something else? What was calling it and what was it calling? I just can't seem to find any way to drill down to deeper levels like there is in Quantify or the Perl profiler.
I don't have experience with VisualVM -- but JRockit's profiler does provide this information; you may consider using it instead.
Update: a question with a list of java profilers can be found here, for users with sufficient rep to view deleted questions.