When I measure the throughput of my Java application, I see a 50% performance increase over time:
You could try adapting your app to run it with Nailgun. Instead of invoking your app against a fresh JVM each time you invoke it against a Nailgun server which is a long-lived JVM. The second time you invoke your app, the nailgun JVM will have optimized the paths in your classes and should therefore execute a lot faster than it would from fresh.